Hemicellulase

ABSTRACT

Hemicellulase that degrades corn non-starch polysaccharides (“NSP”), DNA encoding the same, and a method of using the hemicellulase and its DNA are provided. Proteins having hemicellulase activity such as Xyn5A, Xyn10B, Xyn11A, Xyn30A, and Xyn43A are described.

This application is a Continuation of, and claims priority under 35U.S.C. § 120 to, U.S. patent application Ser. No. 16/266,542, filed Feb.4, 2019, now allowed, which was a Continuation of, and claimed priorityunder 35 U.S.C. § 120 to, International Application No.PCT/JP2017/028415, filed Aug. 4, 2017, and claimed priority therethroughunder 35 U.S.C. § 119 to Japanese Patent Application No. 2016-154514,filed Aug. 5, 2016, the entireties of which are incorporated byreference herein. Also, the Sequence Listing filed electronicallyherewith is hereby incorporated by reference (File name:2020-10-30T_US-590C_Seq_List; File Size: 100 KB; Date recorded: Oct. 30,2020).

BACKGROUND OF THE INVENTION Field of the Invention

The present invention relates to a hemicellulase, DNA encoding it, andmethods of using them.

Brief Description of the Related Art

Recently, the production of biofuels utilizing the energy provided bybiomass, such as cereals, has become of interest. Furthermore, effectiveuse of byproducts of these processes is necessary from the viewpoint ofeffectiveness and problems such as competition with foods. Examples ofsuch byproducts can include dried distiller grains with solubles, alsocalled “DDGS”. DDGS is obtained by ethanol fermentation using starch ofa cereal as the carbon source, adding soluble substances that arepresent in the fermentation broth other than ethanol to the residueafter the distillation of ethanol, and drying the mixture. Since thetypical chosen cereal is corn, DDGS can also be referred to as corndistillers grain. Since DDGS contains abundant proteins and lipids, itis used as a raw material in mixed feeds. However, saccharides in DDGSmainly are non-starch polysaccharides (“NSP”), also referred to asdietary fiber, such as cellulose and hemicellulose, and hence,utilization of DDGS is restricted. The term “hemicellulose” collectivelycan refer to polysaccharides that can be extracted from plant tissueswith alkali, and includes xylan, arabinoxylan, xyloglucan, glucomannan,etc.

Regarding degradation of hemicellulose, for example, Rose et al. (FoodAnal. Methods, 4:66-72 (2011)) describes solubilization of insolublearabinoxylan by two kinds of xylanases produced by Aspergillus oryzae,which belong to Glucoside Hydrolase (GH) families 10 and 11,respectively. While these xylanases show an activity against oat branand wheat bran, the activity thereof against corn bran is only about1/100 of that against oat bran or wheat bran.

As xylanases solubilizing arabinoxylan from corn NSP, WO2014/020142describes xylanase derived from Fusarium verticillioides, andWO2014/020143 describes xylanase derived from Aspergillus clavatus.

As enzymes releasing monosaccharides from corn NSP, US2016-0150807Adescribes alpha-xylosidase derived from Bacteroides ovatus.

There are many reports about xylanases produced by Paenibacillusbacteria. For example, WO2008/037757 describes xylanase derived from P.pabuli. While this xylanase was confirmed to show an insolublearabinoxylan degradation activity against NSP of wheat and barley, it isunknown whether it shows an activity against corn NSP.

Sakka et al. (Appl. Environ. Microbiol., 77(12):4260-4263 (2011))describes that 3CBM (3 carbohydrate-binding module) of xylanase derivedfrom P. curdlanolyticus contributes degradation of insolublearabinoxylan.

SUMMARY OF THE INVENTION

It is as aspect of the present invention to provide a hemicellulase,specifically a hemicellulase that can degrade corn NSP, DNA encoding it,and methods using both. Novel hemicellulases are described that candegrade corn NSP from Paenibacillus bacteria.

It is an aspect of the present invention to provide a protein selectedfrom the group consisting of: (A1) a protein comprising the amino acidsequence of positions 1 to 535 of SEQ ID NO: 4, positions 1 to 536 ofSEQ ID NO: 26, positions 1 to 536 of SEQ ID NO: 28, or positions 1 to536 of SEQ ID NO: 30, wherein said protein has hemicellulase activity;(A2) a protein comprising the amino acid sequence of positions 1 to 535of SEQ ID NO: 4, positions 1 to 536 of SEQ ID NO: 26, positions 1 to 536of SEQ ID NO: 28, or positions 1 to 536 of SEQ ID NO: 30, but whichincludes substitution, deletion, insertion, and/or addition of 1 to 10amino acid residues, wherein said protein has hemicellulase activity;(A3) a protein comprising an amino acid sequence showing an identity of90% or higher to the amino acid sequence of positions 1 to 535 of SEQ IDNO: 4, positions 1 to 536 of SEQ ID NO: 26, positions 1 to 536 of SEQ IDNO: 28, or positions 1 to 536 of SEQ ID NO: 30, wherein said protein hashemicellulase activity; (B1) a protein comprising the amino acidsequence of positions 1 to 448 of SEQ ID NO: 6, wherein said protein hashemicellulase activity; (B2) a protein comprising the amino acidsequence of positions 1 to 448 of SEQ ID NO: 6, but which includessubstitution, deletion, insertion, and/or addition of 1 to 10 amino acidresidues, wherein said protein has hemicellulase activity; (B3) aprotein comprising an amino acid sequence showing an identity of 90% orhigher to the amino acid sequence of positions 1 to 448 of SEQ ID NO: 6,wherein said protein has hemicellulase activity; (C1) a proteincomprising the amino acid sequence of positions 1 to 183 of SEQ ID NO:9, wherein said protein has hemicellulase activity; (C2) a proteincomprising the amino acid sequence of positions 1 to 183 of SEQ ID NO:9, but which includes substitution, deletion, insertion, and/or additionof 1 to 10 amino acid residues, wherein said protein has hemicellulaseactivity; (C3) a protein comprising an amino acid sequence showing anidentity of 90% or higher to the amino acid sequence of positions 1 to183 of SEQ ID NO: 9, wherein said protein has hemicellulase activity;(D1) a protein comprising the amino acid sequence of positions 1 to 527of SEQ ID NO: 12, positions 1 to 529 of SEQ ID NO: 32, or positions 1 to390 of SEQ ID NO: 34, wherein said protein has hemicellulase activity;(D2) a protein comprising the amino acid sequence of positions 1 to 527of SEQ ID NO: 12, positions 1 to 529 of SEQ ID NO: 32, or positions 1 to390 of SEQ ID NO: 34, but which includes substitution, deletion,insertion, and/or addition of 1 to 10 amino acid residues, wherein saidprotein has hemicellulase activity; (D3) a protein comprising an aminoacid sequence showing an identity of 90% or higher to the amino acidsequence of positions 1 to 527 of SEQ ID NO: 12, positions 1 to 529 ofSEQ ID NO: 32, or positions 1 to 390 of SEQ ID NO: 34, wherein saidprotein has hemicellulase activity; (E1) a protein comprising the aminoacid sequence of positions 1 to 608 of SEQ ID NO: 14, wherein saidprotein has hemicellulase activity; (E2) a protein comprising the aminoacid sequence of positions 1 to 608 of SEQ ID NO: 14, but which includessubstitution, deletion, insertion, and/or addition of 1 to 10 amino acidresidues, wherein said protein has hemicellulase activity; and (E3) aprotein comprising an amino acid sequence showing an identity of 90% orhigher to the amino acid sequence of positions 1 to 608 of SEQ ID NO:14, wherein said protein has hemicellulase activity.

It is a further aspect of the present invention to provide the proteinas described above, wherein the protein is selected from the groupconsisting of (A1), (A2), (A3), (B1), (B2), (B3), (C1), (C2), (C3),(D1), (D2), and (D3), and wherein said protein has beta-1,4-xylanaseactivity.

It is a further aspect of the present invention to provide the proteinas described above, wherein the proteins of (A2) and (A3) comprise theamino acid sequence of positions 218 to 239 of SEQ ID NO: 4.

It is a further aspect of the present invention to provide the proteinas described above, wherein the protein is selected from the groupconsisting of (E1), (E2), and (E3), and wherein said protein hasalpha-L-arabinofuranosidase activity.

It is a further aspect of the present invention to provide ahemicellulase preparation comprising at least one protein as describedabove.

It is a further aspect of the present invention to provide thehemicellulase preparation as described above, comprising at least two ofsaid proteins.

It is a further aspect of the present invention to provide thehemicellulase preparation as described above, further comprising aprotein selected from the group consisting of: (F1) a protein comprisingthe amino acid sequence of positions 1 to 469 of SEQ ID NO: 36, whereinsaid protein has a property of enhancing hemicellulase activity; (F2) aprotein comprising the amino acid sequence of positions 1 to 469 of SEQID NO: 36, but which includes substitution, deletion, insertion, and/oraddition of 1 to 10 amino acid residues, wherein said protein has aproperty of enhancing hemicellulase activity; and (F3) a proteincomprising an amino acid sequence showing an identity of 90% or higherto the amino acid sequence of positions 1 to 469 of SEQ ID NO: 36,wherein said protein has a property of enhancing hemicellulase activity.

It is a further aspect of the present invention to provide thehemicellulase preparation as described above, comprising a proteinselected from the group consisting of (A1), (A2), (A3), and combinationsthereof.

It is a further aspect of the present invention to provide a DNAencoding the protein as described above.

It is a further aspect of the present invention to provide a vectorcontaining the DNA as described above.

It is a further aspect of the present invention to provide a host havingenhanced expression of the DNA as described above.

It is a further aspect of the present invention to provide the host asdescribed above, which is a bacterium or a fungus.

It is a further aspect of the present invention to provide a method forproducing a saccharification product, the method comprising: treating ahemicellulosic substrate with the protein as described above.

It is a further aspect of the present invention to provide the method asdescribed above, wherein the hemicellulosic substrate is a biomassresource.

It is a further aspect of the present invention to provide an animalfeed additive comprising at least one protein as described above.

It is a further aspect of the present invention to provide the animalfeed additive as described above, further containing a protein selectedfrom the group consisting of: (F1) a protein comprising the amino acidsequence of positions 1 to 469 of SEQ ID NO: 36, wherein said proteinhas a property of enhancing hemicellulase activity; (F2) a proteincomprising the amino acid sequence of positions 1 to 469 of SEQ ID NO:36, but which includes substitution, deletion, insertion, and/oraddition of 1 to 10 amino acid residues, wherein said protein has aproperty of enhancing hemicellulase activity; and (F3) a proteincomprising an amino acid sequence showing an identity of 90% or higherto the amino acid sequence of positions 1 to 469 of SEQ ID NO: 36,wherein said protein has a property of enhancing hemicellulase activity.

It is a further aspect of the present invention to provide an animalfeed comprising at least one protein as described above.

It is a further aspect of the present invention to provide the animalfeed as described above, further containing a protein selected from thegroup consisting of: (F1) a protein comprising the amino acid sequenceof positions 1 to 469 of SEQ ID NO: 36, wherein said protein has aproperty of enhancing hemicellulase activity; (F2) a protein comprisingthe amino acid sequence of positions 1 to 469 of SEQ ID NO: 36, butwhich includes substitution, deletion, insertion, and/or addition of 1to 10 amino acid residues, wherein said protein has a property ofenhancing hemicellulase activity; and (F3) a protein comprising an aminoacid sequence showing an identity of 90% or higher to the amino acidsequence of positions 1 to 469 of SEQ ID NO: 36, wherein said proteinhas a property of enhancing hemicellulase activity.

It is a further aspect of the present invention to provide Paenibacillussp. AJ111229 strain (NITE BP-02241).

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 shows a chromatogram of a reaction mixture of wheat arabinoxylandegradation by Xyn43A.

FIG. 2 shows a diagram showing release of soluble arabinoxylan from cornDDGS by various enzymes (enzyme concentration=10 μg/mL).

FIG. 3 shows a diagram showing release of soluble arabinoxylan from cornDDGS under different enzyme concentrations.

FIG. 4 shows a diagram showing release of soluble arabinoxylan from cornDDGS by various enzymes (enzyme concentration=1 μg/mL).

FIG. 5 shows a diagram showing release of soluble arabinoxylan from cornDDGS by various enzymes (enzyme concentration=1 μg/mL).

FIG. 6 shows a diagram showing degradation of wheat arabinoxylan byvarious enzymes.

FIG. 7 shows a diagram showing release of soluble arabinoxylan from cornNSP by various enzymes.

DETAILED DESCRIPTION OF EXEMPLARY EMBODIMENTS

<1> Hemicellulase and DNA Encoding it

The present invention provides a hemicellulase and DNA encoding it. Thishemicellulase can also be referred to as “hemicellulase as describedherein”. This DNA can also be referred to as “DNA as described herein”.

The term “hemicellulase” collectively can refer to enzymes hydrolyzinghemicellulose (EC 3.2.1.8 or EC 3.2.1.89). Hemicellulose is apolysaccharide that can be extracted from plant tissues with alkali.Major examples of hemicellulose can include xylan, arabinoxylan,xyloglucan, glucomannan, etc. An activity of hydrolyzing hemicellulosecan also be referred to as “hemicellulase activity”.

The hemicellulase as described herein may have at least an activity ofdegrading xylan (xylanase activity) and/or an activity of degradingarabinoxylan (arabinoxylanase activity). A hemicellulase having xylanaseactivity and a hemicellulase having arabinoxylanase activity can also bereferred to as “xylanase” (EC 3.2.1.8) and “arabinoxylanase”,respectively. Hence, the hemicellulase as described herein may bexylanase (EC 3.2.1.8) or arabinoxylanase. The hemicellulase as describedherein may have, specifically, an activity of cleavingbeta-1,4-glycoside bond between xylose residues forming a backbone ofxylan or arabinoxylan (beta-1,4-xylanase activity). A hemicellulasehaving beta-1,4-xylanase activity can also be referred to as“beta-1,4-xylanase (endo-1,4-beta-xylanase)”. Hence, the hemicellulaseas described herein may also be beta-1,4-xylanase(endo-1,4-beta-xylanase). The xylan and arabinoxylan can, for example,be derived from various plants and be insoluble or soluble. Examples ofthe plants can include, for example, corn, wheat, and beechwood. Xylosefrom the main chain of corn arabinoxylan has been modified with4-O-methyl glucuronic acid as well as arabinose, and hence, cornarabinoxylan can also be referred to as “glucuronoarabinoxylan”. Thehemicellulase as described herein may have, specifically, an activity ofcleaving the beta-1,4-glycoside bond between xylose residues that formthe backbone of glucuronoarabinoxylan such as corn arabinoxylan(glucuronoarabinoxylan endo-1,4-beta-xylanase activity). A hemicellulasehaving glucuronoarabinoxylan endo-1,4-beta-xylanase activity can also bereferred to as “glucuronoarabinoxylan endo-1,4-beta-xylanase” (EC3.2.1.136). Hence, the hemicellulase as described herein may also beglucuronoarabinoxylan endo-1,4-beta-xylanase (EC 3.2.1.136). Thehemicellulase as described herein may also have an activity of releasingside chain arabinose from arabinoxylan (alpha-L-arabinofuranosidaseactivity). A hemicellulase having alpha-L-arabinofuranosidase activitycan also be referred to as “alpha-L-arabinofuranosidase” (EC 3.2.1.55).Hence, the hemicellulase as described herein may also bealpha-L-arabinofuranosidase (EC 3.2.1.55). The hemicellulase asdescribed herein may have, particularly, an activity of degrading cornNSP, specifically an activity of degrading arabinoxylan contained incorn NSP, more specifically an activity of degrading insolublearabinoxylan contained in corn NSP. The term “an activity of degradinginsoluble arabinoxylan (insoluble arabinoxylan degradation activity)”may mean, particularly, an activity of generating soluble arabinoxylanfrom insoluble arabinoxylan.

The activities exemplified above each are an example of hemicellulaseactivity. The hemicellulase as described herein may have one of thesehemicellulase activities, or may have two or more of these hemicellulaseactivities.

Hemicellulase activity can be measured by incubating an enzyme with asubstrate, and measuring enzyme- and substrate-dependent generation of aproduct. The substrate and product can be appropriately chosen accordingto the kind of hemicellulase activity.

For example, xylanase activity and arabinoxylanase activity can bedetected or measured by carrying out an enzymatic reaction using xylanand arabinoxylan as the substrates respectively, and measuring thegeneration amount of reducing termini. For example, beta-1,4-xylanaseactivity can be detected or measured by carrying out an enzymaticreaction using xylan or arabinoxylan as the substrate, and measuring thegeneration amount of reducing termini. For example,glucuronoarabinoxylan endo-1,4-beta-xylanase activity can be detected ormeasured by carrying out an enzymatic reaction usingglucuronoarabinoxylan as the substrate, and measuring the generationamount of reducing termini. The amount of reducing termini can bemeasured by known methods such as dinitrosalicylic acid (DNS) method andSomogyi-Nelson method.

Furthermore, for example, alpha-L-arabinofuranosidase activity can bedetected or measured by carrying out an enzymatic reaction usingarabinoxylan as the substrate, and measuring the released amount ofarabinose. The amount of arabinose can be measured by known methods suchas ion chromatography.

Furthermore, for example, insoluble arabinoxylan degradation activitycan be detected or measured by carrying out an enzymatic reaction usinginsoluble arabinoxylan as the substrate, and measuring the generationamount of soluble arabinoxylan. As the insoluble arabinoxylan, forexample, corn NSP or corn DDGS (corn distillers grain from which solublearabinoxylan has been removed) can be used. Specific examples of methodsfor detecting or measuring insoluble arabinoxylan degradation activitycan include methods described in Example 3 or 7 below. The amount ofsoluble arabinoxylan can be measured by known methods such asphloroglucinol-acetate method (Sakka M. et al., Appl. Environ.Microbiol., 77(12):4260-4263, 2011).

Specific examples of the hemicellulase as described herein can include aprotein having the amino acid sequence of

(1) positions 1 to 535 of SEQ ID NO: 4, positions 1 to 536 of SEQ ID NO:26, positions 1 to 536 of SEQ ID NO: 28, or positions 1 to 536 of SEQ IDNO: 30,

(2) positions 1 to 448 of SEQ ID NO: 6,

(3) positions 1 to 183 of SEQ ID NO: 9,

(4) positions 1 to 527 of SEQ ID NO: 12, positions 1 to 529 of SEQ IDNO: 32, or positions 1 to 390 of SEQ ID NO: 34, or

(5) positions 1 to 608 of SEQ ID NO: 14, and having hemicellulaseactivity. Proteins having the aforementioned amino acid sequences of (1)to (5) are also referred to as Xyn5A, Xyn10B, Xyn11A, Xyn30A, andXyn43A, respectively. The expression “a gene or protein has a nucleotideor amino acid sequence” can mean that a gene or protein includes thenucleotide or amino acid sequence unless otherwise stated, and alsoincludes that the gene or protein includes only the nucleotide or aminoacid sequence.

Xyn5A, Xyn10B, Xyn11A, Xyn30A, and Xyn43A may have xylanase activityand/or arabinoxylanase activity.

Xyn5A, Xyn10B, Xyn11A, and Xyn30A may have, specifically,beta-1,4-xylanase activity. Xyn5A, Xyn10B, and Xyn11A may havebeta-1,4-xylanase activity, particularly, against arabinoxylan. Xyn10B,Xyn11A, and Xyn30A may have beta-1,4-xylanase activity, particularly,against xylan. In an embodiment, Xyn10B and Xyn11A have an activity ofdegrading both beechwood xylan and insoluble wheat xylan. In anembodiment, Xyn5A has an activity of degrading insoluble wheat xylan,while it does not have an activity of degrading beechwood xylan. In anembodiment, Xyn30A does not have an activity of degrading insolublewheat xylan, while it has an activity of degrading beechwood xylan.Xyn5A, Xyn10B, Xyn11A, and Xyn30A may have an activity of degrading cornNSP, specifically an activity of degrading arabinoxylan contained incorn NSP, more specifically an activity of degrading insolublearabinoxylan contained in corn NSP.

Xyn43A may have alpha-L-arabinofuranosidase activity (EC 3.2.1.55).

The hemicellulase as described herein may also be a variant of any ofthe proteins having the aforementioned amino acid sequences, so long asthe hemicellulase activity is maintained. Such a variant of whichhemicellulase activity is maintained can also be referred to as“conservative variant”. Furthermore, the hemicellulase as describedherein may also be a fusion protein of any of proteins having theaforementioned amino acid sequences or variants thereof with anotherpeptide. A protein defined with the aforementioned protein name caninclude not only the proteins exemplified above, but also can includeconservative variants thereof, and fusion proteins of any of thoseproteins or variants thereof with another peptide. That is, for example,the term “Xyn5A” can include not only Xyn5A having the amino acidsequence of positions 1 to 535 of SEQ ID NO: 4, positions 1 to 536 ofSEQ ID NO: 26, positions 1 to 536 of SEQ ID NO: 28, or positions 1 to536 of SEQ ID NO: 30, but also can include conservative variants thereofand, and fusion proteins of any of those proteins or variants thereofwith another peptide.

Hereinafter, examples of conservative variants of hemicellulase will bedescribed.

The hemicellulase as described herein may be a protein having any of theaforementioned amino acid sequences of (1) to (5), but which includessubstitution, deletion, insertion, and/or addition of one or severalamino acid residues at one or several positions, so long ashemicellulase activity is maintained. Although the number meant by theterm “one or several” mentioned above may differ depending on thepositions of amino acid residues in the three-dimensional structure ofthe protein or the types of amino acid residues, specifically, it maybe, for example, 1 to 10, 1 to 8, 1 to 5, or 1 to 3.

The aforementioned substitution, deletion, insertion, or addition of oneor several amino acid residues are/is a conservative mutation thatmaintains the normal function of the protein. Typical examples of theconservative mutation are conservative substitutions. The conservativesubstitution is a mutation wherein substitution takes place mutuallyamong Phe, Trp, and Tyr, if the substitution site is an aromatic aminoacid; among Leu, Ile, and Val, if it is a hydrophobic amino acid;between Gln and Asn, if it is a polar amino acid; among Lys, Arg, andHis, if it is a basic amino acid; between Asp and Glu, if it is anacidic amino acid; and between Ser and Thr, if it is an amino acidhaving a hydroxyl group. Examples of substitutions considered asconservative substitutions can include, specifically, substitution ofSer or Thr for Ala, substitution of Gln, His, or Lys for Arg,substitution of Glu, Gln, Lys, His, or Asp for Asn, substitution of Asn,Glu, or Gln for Asp, substitution of Ser or Ala for Cys, substitution ofAsn, Glu, Lys, His, Asp, or Arg for Gln, substitution of Gly, Asn, Gln,Lys, or Asp for Glu, substitution of Pro for Gly, substitution of Asn,Lys, Gln, Arg, or Tyr for His, substitution of Leu, Met, Val, or Phe forIle, substitution of Ile, Met, Val, or Phe for Leu, substitution of Asn,Glu, Gln, His, or Arg for Lys, substitution of Ile, Leu, Val, or Phe forMet, substitution of Trp, Tyr, Met, Ile, or Leu for Phe, substitution ofThr or Ala for Ser, substitution of Ser or Ala for Thr, substitution ofPhe or Tyr for Trp, substitution of His, Phe, or Trp for Tyr, andsubstitution of Met, Ile, or Leu for Val. Furthermore, suchsubstitution, deletion, insertion, addition, or inversion of amino acidresidues as mentioned above includes a naturally occurring mutation dueto an individual difference, or a difference of species of the organismfrom which the protein is derived (mutant or variant).

The hemicellulase as described herein may also be a protein having anamino acid sequence showing a high homology, for example, a homology of90% or more, 95% or more, 97% or more, or 99% or more, to the totalamino acid sequence of any of the aforementioned amino acid sequences of(1) to (5), so long as hemicellulase activity is maintained. “Homology”can mean “identity”.

The hemicellulase as described herein may include a common sequence ofthe aforementioned hemicellulases. For example, Xyn5A may include acommon sequence of the aforementioned Xyn5A, that is, a common sequenceof two or more, or all of the amino acid sequences of positions 1 to 535of SEQ ID NO: 4, positions 1 to 536 of SEQ ID NO: 26, positions 1 to 536of SEQ ID NO: 28, and positions 1 to 536 of SEQ ID NO: 30. Such a commonsequence can be determined by, for example, alignment. Specific examplesof a common sequence of Xyn5A can include, for example, the amino acidsequence of positions 218 to 239 of SEQ ID NO: 4.

The hemicellulase as described herein may also be a fusion protein withanother peptide. Examples of the other peptide can include markerpeptides (marker proteins), peptide tags, and pro sequences or pre-prosequences such as secretion signal peptides. That is, examples of thefusion protein can include, for example, precursors of hemicellulase.One kind of peptide or two or more kinds of peptides may be fused tohemicellulase. In cases where hemicellulase is a fusion protein with asignal peptide, the signal peptide may be cleaved after expression ofthe hemicellulase in a host cell capable of secretory production, andthereby only the hemicellulase moiety may be secreted outside the cell.In addition, even in cases where the hemicellulase is not secreted, thesignal peptide may be cleaved in a host cell, and a mature protein maybe generated. In cases where hemicellulase is a fusion protein, theaforementioned homology represents homology in the residual portion ofhemicellulase from which such other peptide have been removed (e.g.mature protein moiety).

Marker peptides are not particularly limited, so long as they arepeptides that can function as a marker, and specific examples thereofcan include, for example, alkaline phosphatase, Fc region of antibody,HRP, GFP, etc. Specific examples of peptide tags can include, but arenot particularly limited to, known peptide tags such as Myc tag, Histag, FLAG tag, and GST tag. Secretion signal peptides are notparticularly limited, so long as they can function in a host forexpressing DNA encoding hemicellulase, and examples thereof can include,for example, secretion signal peptides of Sec or Tat secretion systemderived from coryneform bacteria for cases of using a coryneformbacterium as a host (see WO01/23591 and WO2005/103278), as well assecretion signal peptides of hemicellulase. The fusion protein can beproduced in a conventional manner.

The DNA as described herein is not particularly limited, so long as itencodes the hemicellulase as described herein. Specific examples of theDNA as described herein can include DNAs encoding the aforementionedamino acid sequences of (1) to (5). More specific examples of the DNA asdescribed herein can include DNAs having the nucleotide sequence ofpositions 115 to 1719 of SEQ ID NO: 3, positions 88 to 1695 of SEQ IDNO: 27, positions 97 to 1704 of SEQ ID NO: 29, or positions 88 to 1695of SEQ ID NO: 31 (encoding Xyn5A); the nucleotide sequence of positions136 to 1479 of SEQ ID NO: 5 (encoding Xyn10B); the nucleotide sequenceof positions 85 to 633 of SEQ ID NO: 8 (encoding Xyn11A); positions 109to 1689 of SEQ ID NO: 11, the nucleotide sequence of positions 91 to1677 of SEQ ID NO: 33, or positions 91 to 1260 of SEQ ID NO: 35(encoding Xyn30A); and the nucleotide sequence of positions 79 to 1902of SEQ ID NO: 13 (encoding Xyn43A). The DNA as described herein may alsobe DNA encoding a conservative variant of any of proteins having theseamino acid sequences. The DNA as described herein may also be DNAencoding a fusion protein of any of proteins having these amino acidsequences or variants thereof with another peptide. The DNA as describedherein may further include a start codon at 5′ terminal side of any ofthe aforementioned nucleotide sequences. The DNA as described herein mayfurther include a stop codon at 3′ terminal side of any of theaforementioned nucleotide sequences. The DNA as described herein may beadded with a sequence such as promoter.

The DNA as described herein is not limited to those DNAs, and may alsobe DNA in which codons encoding amino acids in the coding region havebeen replaced with equivalent codons encoding the same amino acids. Thatis, the DNA as described herein may also be a variant of any of the DNAsexemplified above due to the degeneracy of codons.

The DNA as described herein also includes DNA that is able to hybridizeunder stringent conditions with a probe having a nucleotide sequencecomplementary to any of the aforementioned nucleotide sequences or witha probe that can be prepared from such a complementary sequence, andencodes a protein having hemicellulase activity. The term “stringentconditions” can refer to conditions under which a so-called specifichybrid is formed, and a non-specific hybrid is not formed. Examples ofthe stringent conditions can include those under which highly homologousDNAs hybridize to each other, for example, DNAs not less than 50%, 65%,80% 90%, 95%, 97%, or 99% homologous, hybridize to each other, and DNAsless homologous than the above do not hybridize to each other, orconditions of washing of typical Southern hybridization, i.e.,conditions of washing once, or 2 or 3 times, at a salt concentration andtemperature corresponding to 1×SSC, 0.1% SDS at 60° C.; 0.1×SSC, 0.1%SDS at 60° C.; or 0.1×SSC, 0.1% SDS at 68° C. Furthermore, for example,when a DNA fragment having a length of about 300 bp is used as theprobe, the washing conditions of the hybridization may be, for example,50° C., 2×SSC and 0.1% SDS.

The percentage of the sequence identity between two sequences can bedetermined by, for example, using a mathematical algorithm. Non-limitingexamples of such a mathematical algorithm can include the algorithm ofMyers and Miller (1988) CABIOS 4:11-17, the local homology algorithm ofSmith et al (1981) Adv. Appl. Math. 2:482, the homology alignmentalgorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453, themethod for searching homology of Pearson and Lipman (1988) Proc. Natl.Acad. Sci. 85:2444-2448, and an modified version of the algorithm ofKarlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264, such asthat described in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA90:5873-5877.

By using a program based on such a mathematical algorithm, sequencecomparison (i.e. alignment) for determining the sequence identity can beperformed. The program can be appropriately executed by a computer.Examples of such a program can include, but are not limited to, CLUSTALof PC/Gene program (available from Intelligenetics, Mountain View,Calif.), ALIGN program (Version 2.0), and GAP, BESTFIT, BLAST, FASTA,and TFASTA of Wisconsin Genetics Software Package, Version 8 (availablefrom Genetics Computer Group (GCG), 575 Science Drive, Madison, Wis.,USA). Alignment using these programs can be performed by using, forexample, initial parameters. The CLUSTAL program is well described inHiggins et al. (1988) Gene 73:237-244, Higgins et al. (1989) CABIOS5:151-153, Corpet et al. (1988) Nucleic Acids Res. 16:10881-90, Huang etal. (1992) CABIOS 8:155-65, and Pearson et al. (1994) Meth. Mol. Biol.24:307-331.

In order to obtain a nucleotide sequence homologous to a targetnucleotide sequence, in particular, for example, BLAST nucleotide searchcan be performed by using BLASTN program with score of 100 and wordlength of 12. In order to obtain an amino acid sequence homologous to atarget protein, in particular, for example, BLAST protein search can beperformed by using BLASTX program with score of 50 and word length of 3.See ncbi.nlm.nih.gov for BLAST nucleotide search and BLAST proteinsearch. In addition, Gapped BLAST (BLAST 2.0) can be used in order toobtain an alignment including gap(s) for the purpose of comparison. Inaddition, PSI-BLAST (BLAST 2.0) can be used in order to performrepetitive search for detecting distant relationships between sequences.See Altschul et al. (1997) Nucleic Acids Res. 25:3389 for Gapped BLASTand PSI-BLAST. When using BLAST, Gapped BLAST, or PSI-BLAST, forexample, initial parameters of each program (e.g. BLASTN for nucleotidesequences, and BLASTX for amino acid sequences) can be used. Alignmentcan also be manually performed.

The sequence identity between two sequences is calculated as the ratioof residues matching in the two sequences when aligning the twosequences so as to fit maximally with each other.

<2> Enzyme Enhancing Hemicellulase Activity and DNA Encoding it

The present invention provides an enzyme enhancing hemicellulaseactivity and DNA encoding it.

Specific examples of the enzyme enhancing hemicellulase activity caninclude a protein that includes the amino acid sequence of positions 1to 469 of SEQ ID NO: 36, and having a property of enhancinghemicellulase activity. A protein having this amino acid sequence can bereferred to as Abf51A.

The type and number of hemicellulase activity/activities enhanced by theenzyme enhancing hemicellulase activity are not particularly limited.The enzyme enhancing hemicellulase activity may have a property ofenhancing, for example, one or more of the hemicellulase activitiesexemplified above. The enzyme enhancing hemicellulase activity may havea property of enhancing, specifically, for example, an activity ofdegrading wheat arabinoxylan and/or an activity of degrading corn NSP.The enzyme enhancing hemicellulase activity may also have a property ofenhancing, for example, activity/activities of one or more of Xyn5A,Xyn10B, Xyn11A, Xyn30A, and/or Xyn43A. The enzyme enhancinghemicellulase activity may also have a property of enhancing,specifically, for example, an activity of Xyn5A.

The enzyme enhancing hemicellulase activity may or may not havehemicellulase activity.

The enzyme enhancing hemicellulase activity may also be a variant of anyof proteins having the aforementioned amino acid sequence, so long asthe property of enhancing hemicellulase activity is maintained. To sucha variant, the descriptions concerning variants of hemicellulase can besimilarly applied.

Whether a protein has a property of enhancing hemicellulase activity canbe confirmed by carrying out an enzymatic reaction using a hemicellulasein the presence and absence of the protein, and comparing hemicellulaseactivities.

Specific examples of the DNA encoding the enzyme enhancing hemicellulaseactivity can include DNAs encoding the aforementioned amino acidsequence. More specific examples of the DNA encoding the enzymeenhancing hemicellulase activity can include DNAs having the nucleotidesequence of positions 82 to 1488 of SEQ ID NO: 37 (encoding Abf51A). TheDNA encoding the enzyme enhancing hemicellulase activity may also be DNAencoding a conservative variant of any of proteins having theaforementioned amino acid sequence. The DNA encoding the enzymeenhancing hemicellulase activity may also be DNA encoding a fusionprotein of any of proteins having the aforementioned amino acid sequenceor variants thereof with another peptide. The DNA encoding the enzymeenhancing hemicellulase activity may further include a start codon at 5′terminal side of the aforementioned nucleotide sequence. The DNAencoding the enzyme enhancing hemicellulase activity may further includea stop codon at 3′ terminal side of the aforementioned nucleotidesequence. The DNA encoding the enzyme enhancing hemicellulase activitymay be added with a sequence such as promoter. In addition, to the DNAencoding the enzyme enhancing hemicellulase activity, the descriptionsconcerning the DNA as described herein can be similarly applied.

<3> Production of Hemicellulase

The hemicellulase as described herein can be obtained from, for example,a culture broth of the Paenibacillus sp. H2C strain as shown in Example3. The strain H2C was deposited at the independent administrativeagency, National Institute of Technology and Evaluation, PatentMicroorganisms Depositary (NPMD; #122, 2-5-8 Kazusakamatari,Kisarazu-shi, Chiba-ken, 292-0818) on Apr. 15, 2016 under the provisionsof the Budapest Treaty, and assigned an accession number of NITEBP-02241 with an identification reference of AJ111229.

The hemicellulase as described herein can be produced by making anappropriate host express DNA encoding it (the DNA as described herein).The DNA as described herein may also be referred to as “hemicellulasegene”. The hemicellulase gene can be prepared by chemical synthesis,since the amino acid sequence of the hemicellulase as described hereinhas been identified. The DNA as described herein can also be cloned fromthe Paenibacillus sp. H2C strain on the basis of the sequence thereof bythe PCR method etc.

The obtained gene can be used as it is, or after being modified asrequired. That is, a variant of a gene may be obtained by modifying thegene. The gene can be modified by a known method. For example, it can bemodified by site-specific mutagenesis, or an objective mutation can beintroduced into a target site of DNA. That is, for example, a codingregion of a gene can be modified by the site-specific mutagenesis methodso that a specific site of the encoded protein can include substitution,deletion, insertion, and/or addition of amino acid residues. Examples ofthe site-specific mutagenesis method can include a method using PCR(Higuchi, R., 61, in PCR Technology, Erlich, H. A. Eds., Stockton Press,1989; Carter P., Meth., in Enzymol., 154, 382, 1987), and a method ofusing a phage (Kramer, W. and Frits, H. J., Meth. in Enzymol., 154, 350,1987; Kunkel, T. A. et al., Meth. in Enzymol., 154, 367, 1987).Alternatively, a variant of a gene may also be totally synthesized.

In particular, a host having an enhanced expression of a hemicellulasegene can be used for production of the hemicellulase as describedherein. The term “host having an enhanced expression of a hemicellulasegene” can refer to a host introduced with a hemicellulase gene in such amanner that the gene can be expressed, or a host that is a microorganismhaving a hemicellulase gene and in which expression of the gene has beenenhanced.

The host is not particularly limited, so long as it can express thehemicellulase. Examples of the host can include, for example, bacteria,fungi, plant cells, insect cells, and animal cells. Preferred examplesof the host can include microorganisms such as bacteria and fungi.

Examples of the bacteria can include gram-negative bacteria andgram-positive bacteria. Examples of the gram-negative bacteria caninclude, for example, bacteria belonging to the familyEnterobacteriaceae, such as Escherichia bacteria, Enterobacter bacteria,and Pantoea bacteria. Examples of the gram-positive bacteria can includeBacillus bacteria, coryneform bacteria such as Corynebacterium bacteria,and actinomycetes. Examples of the Escherichia bacteria can include, forexample, Escherichia coli. Examples of the Corynebacterium bacteria caninclude, for example, Corynebacterium glutamicum and Corynebacteriumammoniagenes (Corynebacterium stationis). Specific examples ofEscherichia coli can include, for example, Escherichia coli K-12 strainssuch as W3110 strain (ATCC 27325) and MG1655 strain (ATCC 47076);Escherichia coli KS strain (ATCC 23506); Escherichia coli B strains suchas BL21(DE3) strain and a recA-strain thereof, BLR(DE3); and derivativestrains thereof.

These strains are available from, for example, the American Type CultureCollection (Address: P.O. Box 1549, Manassas, Va. 20108, United Statesof America). That is, registration numbers are given to the respectivestrains, and the strains can be ordered by using these registrationnumbers (can refer to atcc.org). The registration numbers of the strainsare listed in the catalogue of the American Type Culture Collection.These strains can also be obtained from, for example, the depositoriesat which the strains were deposited. The BL21(DE3) strain is availablefrom, for example, Life Technologies (product number C6000-03).

Methods for introducing the hemicellulase gene into a host are notparticularly limited. In a host, a hemicellulase gene may be harbored insuch a manner that it can be expressed under control of a promoter thatfunctions in the host. In the host, the hemicellulase gene may bepresent on a vector autonomously replicable independent of thechromosome, such as plasmid, or may be introduced into the chromosome.The host may have only one copy of the hemicellulase gene, or may havetwo or more copies of the hemicellulase gene. The host may have only onekind of hemicellulase gene, or may have two or more kinds ofhemicellulase genes.

The promoter for expressing the hemicellulase gene is not particularlylimited so long as it is a promoter that functions in the host. The“promoter that functions in a host” can refer to a promoter that has apromoter activity in the host. The promoter may be a promoter derivedfrom, that is, native to, the host, or may be a heterologous promoter.The promoter may be the native promoter of the hemicellulase gene, ormay be a promoter of another gene. The promoter may be stronger than thenative promoter of the hemicellulase gene. Examples of strong promotersthat function in Enterobacteriaceae bacteria, such as Escherichia coli,can include, for example, T7 promoter, trp promoter, trc promoter, lacpromoter, tac promoter, tet promoter, araBAD promoter, rpoH promoter,msrA promoter, Pm1 promoter (derived from the genus Bifidobacterium), PRpromoter, and PL promoter. Examples of strong promoters that function incoryneform bacteria can include the artificially modified P54-6 promoter(Appl. Microbiol. Biotechnol., 53, 674-679 (2000)), pta, aceA, aceB,adh, and amyE promoters inducible in coryneform bacteria with aceticacid, ethanol, pyruvic acid, or the like, cspB, SOD, and tuf (EF-Tu)promoters, which are potent promoters capable of providing a largeexpression amount in coryneform bacteria (Journal of Biotechnology, 104(2003) 311-323; Appl. Environ. Microbiol., 2005 December; 71(12):8587-96), as well as lac promoter, tac promoter, and trc promoter.Examples of promoters that function in fungi such as Talaromycescellulolyticus can include, for example, glaA promoter, and promoters ofgenes encoding saccharide hydrolases, such as cellulase gene andxylanase gene. Furthermore, as the promoter, a highly-active type of anexisting promoter may also be obtained by using various reporter genes.For example, by making the −35 and −10 regions in a promoter regioncloser to the consensus sequence, the activity of the promoter can beenhanced (WO00/18935). Examples of highly active-type promoter caninclude various tac-like promoters (Katashkina J I et al., RussianFederation Patent Application No. 2006134574) and pnlp8 promoter(WO2010/027045). Methods for evaluating the strength of promoters andexamples of strong promoters are described in the paper of Goldstein etal. (Prokaryotic Promoters in Biotechnology, Biotechnol. Annu. Rev., 1,105-128 (1995)), and so forth.

Also, a terminator for termination of gene transcription may be locateddownstream of the hemicellulase gene. The terminator is not particularlylimited so long as it functions in the bacterium as described herein.The terminator may be a terminator derived from the host, or aheterogenous terminator. The terminator may be the native terminator ofthe hemicellulase gene, or a terminator of another gene. Specificexamples of the terminator can include, for example, T7 terminator, T4terminator, fd phage terminator, tet terminator, and trpA terminator.

The hemicellulase gene can be introduced into a host, for example, byusing a vector containing the gene. A vector containing thehemicellulase gene can also be referred to as an expression vector orrecombinant vector for the hemicellulase gene. The expression vector forthe hemicellulase gene can be constructed by, for example, ligating aDNA fragment containing the hemicellulase gene with a vector thatfunctions in the host. By transforming the host with the expressionvector for the hemicellulase gene, a transformant into which the vectorhas been introduced can be obtained, i.e. the gene can be introducedinto the host. As the vector, a vector autonomously replicable in thecell of the host can be used. The vector can be a multi-copy vector.Furthermore, the vector can have a marker such as an antibioticresistance gene for selection of transformant. Furthermore, the vectormay have a promoter and/or terminator for expressing the introducedgene. The vector may be, for example, a vector derived from a bacterialplasmid, a vector derived from a yeast plasmid, a vector derived from abacteriophage, cosmid, phagemid, or the like. Specific examples of avector autonomously replicable in Enterobacteriaceae bacteria such asEscherichia coli can include, for example, pUC19, pUC18, pHSG299,pHSG399, pHSG398, pBR322, pSTV29 (all of these are available from TakaraBio), pACYC184, pMW219 (NIPPON GENE), pTrc99A (Pharmacia), pPROK seriesvectors (Clontech), pKK233-2 (Clontech), pET series vectors (Novagen),pQE series vectors (QIAGEN), pCold TF DNA (TaKaRa), pACYC seriesvectors, and the broad host spectrum vector RSF1010. Specific examplesof vector autonomously replicable in coryneform bacteria can include,for example, pHM1519 (Agric. Biol. Chem., 48, 2901-2903 (1984)); pAM330(Agric. Biol. Chem., 48, 2901-2903 (1984)); plasmids obtained byimproving these and having a drug resistance gene; plasmid pCRY30described in Japanese Patent Laid-open (Kokai) No. 3-210184; plasmidspCRY21, pCRY2KE, pCRY2KX, pCRY31, pCRY3KE, and pCRY3KX described inJapanese Patent Laid-open (Kokai) No. 2-72876 and U.S. Pat. No.5,185,262; plasmids pCRY2 and pCRY3 described in Japanese PatentLaid-open (Kokai) No. 1-191686; pAJ655, pAJ611, and pAJ1844 described inJapanese Patent Laid-open (Kokai) No. 58-192900; pCG1 described inJapanese Patent Laid-open (Kokai) No. 57-134500; pCG2 described inJapanese Patent Laid-open (Kokai) No. 58-35197; pCG4 and pCG11 describedin Japanese Patent Laid-open (Kokai) No. 57-183799, pVK7 described inJapanese Patent Laid-open (Kokai) No. 10-215883; and pVC7 described inJapanese Patent Laid-open (Kokai) No. 9-070291. Specific examples of avector autonomously replicable in fungi such as Talaromycescellulolyticus can include, for example, pANC202 (J Ind MicrobiolBiotechnol. 2013 August; 40(8):823-30). When the expression vector isconstructed, for example, the hemicellulase gene having a nativepromoter region as it is may be incorporated into a vector, a codingregion of the hemicellulase ligated downstream from such a promoter asmentioned above may be incorporated into a vector, or a coding region ofthe hemicellulase may be incorporated into a vector downstream from apromoter inherently present in the vector.

Vectors, promoters, and terminators available in various microorganismsare disclosed in detail in “Fundamental Microbiology Vol. 8, GeneticEngineering, KYORITSU SHUPPAN CO., LTD, 1987”, and those can be used.

The hemicellulase gene can also be introduced into, for example, achromosome of a host. A gene can be introduced into a chromosome by, forexample, using homologous recombination (Miller, J. H., Experiments inMolecular Genetics, 1972, Cold Spring Harbor Laboratory). Examples ofthe gene transfer method utilizing homologous recombination can include,for example, a method using a linear DNA such as Red-driven integration(Datsenko, K. A., and Wanner, B. L., Proc. Natl. Acad. Sci. USA,97:6640-6645 (2000)), a method of using a plasmid containing atemperature sensitive replication origin, a method of using a plasmidcapable of conjugative transfer, a method of using a suicide vector nothaving a replication origin that functions in a host, and a transductionmethod using a phage. Only one copy, or two or more copies of a gene maybe introduced. For example, by performing homologous recombination usinga sequence which is present in multiple copies on a chromosome as atarget, multiple copies of a gene can be introduced into the chromosome.Examples of such a sequence which is present in multiple copies on achromosome can include repetitive DNAs, and inverted repeats located atthe both ends of a transposon. Alternatively, homologous recombinationmay be performed by using an appropriate sequence on a chromosome suchas a gene unnecessary for production of the objective substance as atarget. Furthermore, a gene can also be randomly introduced into achromosome by using a transposon or Mini-Mu (Japanese Patent Laid-open(Kokai) No. 2-109985, U.S. Pat. No. 5,882,888, EP 805867 B1). When thegene is introduced into a chromosome, for example, the hemicellulasegene having a native promoter region as it is may be incorporated into achromosome, a coding region of the hemicellulase ligated downstream fromsuch a promoter as mentioned above may be incorporated into achromosome, or a coding region of the hemicellulase may be incorporatedinto a chromosome downstream from a promoter inherently present on thechromosome.

In addition, by replacing an expression control sequence such aspromoter of the hemicellulase gene with a more potent expression controlsequence in a Paenibacillus bacterium having this gene, expression ofthe hemicellulase gene can be enhanced.

Introduction of a gene into a chromosome can be confirmed by, forexample, Southern hybridization using a probe having a sequencecomplementary to a part or the whole of the gene, or PCR using primersprepared on the basis of the nucleotide sequence of the gene.

The method for the transformation is not particularly limited, andconventionally known methods can be used. Examples of transformationmethod can include, for example, a method of treating recipient cellswith calcium chloride so as to increase the permeability thereof forDNA, which has been reported for the Escherichia coli K-12 strain(Mandel, M. and Higa, A., J. Mol. Biol., 1970, 53, 159-162), a method ofpreparing competent cells from cells which are in the growth phase,followed by transformation with DNA, which has been reported forBacillus subtilis (Duncan, C. H., Wilson, G. A. and Young, F. E., Gene,1997, 1:153-167), and so forth. Furthermore, as the transformationmethod, there can also be used a method of making DNA-recipient cellsinto protoplasts or spheroplasts, which can easily take up recombinantDNA, followed by introducing a recombinant DNA into the DNA-recipientcells, which is known to be applicable to Bacillus subtilis,actinomycetes, and yeasts (Chang, S. and Choen, S. N., 1979, Mol. Gen.Genet., 168:111-115; Bibb, M. J., Ward, J. M. and Hopwood, O. A., 1978,Nature, 274:398-400; Hinnen, A., Hicks, J. B. and Fink, G. R., 1978,Proc. Natl. Acad. Sci. USA, 75:1929-1933). Furthermore, as thetransformation method, the electric pulse method reported for coryneformbacteria (Japanese Patent Laid-open (Kokai) No. 2-207791) can also beused.

By culturing the host having the hemicellulase gene in a culture medium,the hemicellulase can be expressed. During the culture, the expressionof the hemicellulase gene can be induced as required. Conditions forinduction of gene expression can be appropriately chosen depending onvarious conditions such as the structure of gene expression system.

The culture medium and culture conditions are not particularly limited,so long as the host having the hemicellulase gene can proliferate, andthe hemicellulase can be produced. The culture medium and cultureconditions can be appropriately chosen depending on various conditionssuch as the type of the host. Culture can be carried out, for example,using a usual culture medium under usual conditions used for culturingmicroorganisms such as bacteria and fungi. Regarding specific culturemedium compositions and culture conditions for culturing bacteria, forexample, culture medium compositions and culture conditions used forproduction of various substances using bacteria such as E. coli andcoryneform bacteria can be used as a reference.

As the culture medium, for example, a liquid culture medium containing acarbon source, nitrogen source, phosphate source, sulfur source, andingredients such as other various organic and inorganic ingredients asrequired can be used. The types and concentrations of the culture mediumcomponents can be appropriately chosen by those skilled in the art.

The carbon source is not particularly limited, so long as the hosthaving the hemicellulase gene can utilize it. Specific examples of thecarbon source can include, for example, saccharides such as glucose,fructose, sucrose, lactose, galactose, xylose, arabinose, blackstrapmolasses, hydrolysate of starch, and hydrolysate of biomass, organicacids such as acetic acid, fumaric acid, citric acid, succinic acid, andmalic acid, alcohols such as glycerol, crude glycerol, and ethanol, andaliphatic acids. Examples of the carbon source also can include biomasscontaining a hemicellulose component described below. As the carbonsource, one kind of carbon source may be used, or two or more kinds ofcarbon sources may be used in combination.

Specific examples of the nitrogen source can include, for example,ammonium salts such as ammonium sulfate, ammonium chloride, and ammoniumphosphate, organic nitrogen sources such as peptone, yeast extract, meatextract, corn steep liquor, and soybean protein decomposition product,ammonia, and urea. As the nitrogen source, one kind of nitrogen sourcemay be used, or two or more kinds of nitrogen sources may be used incombination.

Specific examples of the phosphate source can include, for example,phosphate salts such as potassium dihydrogenphosphate and dipotassiumhydrogenphosphate, and phosphoric acid polymers such as pyrophosphoricacid. As the phosphate source, one kind of phosphate source may be used,or two or more kinds of phosphate sources may be used in combination.

Specific examples of the sulfur source can include, for example,inorganic sulfur compounds such as sulfates, thiosulfates, and sulfites,and sulfur-containing amino acids such as cysteine, cystine, andglutathione. As the sulfur source, one kind of sulfur source may beused, or two or more kinds of sulfur sources may be used in combination.

Specific examples of the other various organic and inorganic componentscan include, for example, inorganic salts such as sodium chloride, andpotassium chloride; trace metals such as iron, manganese, magnesium, andcalcium; vitamins such as vitamin B1, vitamin B2, vitamin B6, nicotinicacid, nicotinamide, and vitamin B12; amino acids; nucleic acids; andorganic components containing these such as peptone, casamino acid,yeast extract, and soybean protein decomposition product. As the othervarious organic and inorganic components, one kind of component may beused, or two or more kinds of components may be used in combination.

The culture can be performed, for example, aerobically as aerationculture or shaking culture using a liquid culture medium. The culturetemperature may be, for example, 15 to 43° C. The pH during the culturemay be, for example, 5 to 9. The culture period may be, for example, 2hours to 20 days. The culture can be performed as batch culture,fed-batch culture, continuous culture, or a combination of these. Theculture may also be performed as separate pre-culture and main culture.For example, the pre-culture may be performed on a solid culture mediumsuch as an agar medium, and the main culture may be performed in aliquid culture medium.

By culturing the host having the hemicellulase gene in a culture mediumunder such conditions as mentioned above, a culture broth containing thehemicellulase is obtained. The hemicellulase can be accumulated in, forexample, microbial cells of the host and/or the culture medium. The term“microbial cell” may be appropriately read as “cell” depending on thetype of the host.

Production of the hemicellulase can be confirmed by, for example,measuring hemicellulase activity in an appropriate fraction such asculture supernatant and cell extract.

The hemicellulase may be used in a state that it is contained in theculture broth or the like, or may be separated and purified from theculture broth or the like as required and used as a crude enzymefraction or a purified enzyme.

That is, for example, when the hemicellulase is accumulated in microbialcells of the host, by subjecting the cells to disruption, lysis,extraction, etc. as required, the hemicellulase can be collected. Themicrobial cells can be collected from the culture broth bycentrifugation or the like. Disruption, lysis, extraction, etc. of thecells can be performed by known methods. Examples of such methods caninclude, for example, disruption by ultrasonication, disruption inDyno-Mill, disruption in bead mill, disruption with French press, andlysozyme treatment. One of these methods may be used alone, or two ormore of these methods may be used in combination as required. Also, forexample, when the hemicellulase is accumulated in the culture medium, aculture supernatant can be obtained by centrifugation or the like, andthe hemicellulase can be collected from the culture supernatant.

The hemicellulase can be purified by known methods used for purificationof enzymes. Examples of such methods can include, for example, ammoniumsulfate fractionation, ion exchange chromatography, hydrophobicchromatography, affinity chromatography, gel filtration chromatography,and isoelectric precipitation. One of these methods may be used alone,or two or more of these methods may be used in combination as required.The hemicellulase may be purified to a desired extent.

Not only the purified hemicellulase, but also any fraction containingthe hemicellulase may be used as the “hemicellulase” for such a usepurpose as degradation of hemicellulose. Such a fraction containing thehemicellulase is not particularly limited, so long as it contains thehemicellulase so that the hemicellulase can act on cellulose. Examplesof such a fraction can include, for example, culture broth, culturesupernatant, processed product of microbial cells (disruption product,lysate, extract (cell-free extract). etc.), partially purified products(roughly purified products) of these, and combinations of these. Thesefractions each may be used alone, or may be used together with apurified hemicellulase.

In the culture broth, other enzyme(s) different from the hemicellulaseas described herein may also be produced and accumulated together withthe hemicellulase as described herein. The hemicellulase as describedherein may be collected as a mixture with such other enzyme(s), or maybe collected separately from such other enzyme(s).

The hemicellulase as described herein may be made into a preparation(formulation) as required. That is, the present invention provides ahemicellulase preparation containing the hemicellulase as describedherein. This hemicellulase preparation can also be referred to as“hemicellulase preparation as described herein”. The dosage form of thehemicellulase preparation as described herein is not particularlylimited, and can be appropriately chosen according to various conditionssuch as use purpose of the hemicellulase. Examples of the dosage formcan include, for example, solution, suspension, powder, tablet, pill,and capsule. For preparing such a preparation, for example,pharmaceutically acceptable additives such as excipients, binders,disintegrating agents, lubricants, stabilizers, corrigents, odor-maskingagents, perfumes, diluents, and surfactants can be used.

The type and number of hemicellulase contained in the hemicellulasepreparation as described herein are not particularly limited. The numberof kinds of hemicellulase contained in the hemicellulase preparation asdescribed herein may be one or more, two or more, or three or more.While any hemicellulase included in the hemicellulase as describedherein independently shows hemicellulase activity, a combination of twoor three or more hemicellulases shows an increased specific activity.Hence, a hemicellulase preparation containing a combination of theseenzymes is useful for degradation of hemicellulose. The combination ofenzymes is not particularly limited. Specific examples of thecombination of enzymes can include, for example, combinations of Xyn5Aand Xyn10B; Xyn5A and Xyn30A; Xyn5A and Xyn43A; Xyn10B and Xyn30A;Xyn10B and Xyn43A; and Xyn30A and Xyn43A. The mixing ratio ofhemicellulases in such a preparation is not particularly limited. Incases of a combination of two kinds of enzymes, examples of the mixingratio can include, for example, 95:5 to 5:95, or 70:30 to 30:70, interms of weight ratio.

The hemicellulase preparation as described herein may contain otherenzyme(s) in addition to the hemicellulase as described herein. The typeand number of the other enzyme(s) contained in the hemicellulasepreparation as described herein are not particularly limited. The numberof kinds of the other enzyme(s) contained in the hemicellulasepreparation as described herein may be one or more, two or more, orthree or more. Examples of the other enzymes can include hemicellulasesother than the hemicellulase as described herein. Examples of the otherenzymes also can include saccharide hydrolases other thanhemicellulases, such as cellulase and xylobiase (beta-xylosidase).Examples of the other enzymes also can include the enzyme enhancinghemicellulase activity, such as Abf51A. The combination of thehemicellulase as described herein and other enzyme(s) is notparticularly limited. The combination of the hemicellulase as describedherein and other enzyme(s) may be, for example, a combination by whichthe activity of the hemicellulase as described herein is enhanced.Specific examples of the combination of the hemicellulase as describedherein and other enzyme(s) can include, for example, a combination ofone or more of Xyn5A, Xyn10B, Xyn11A, Xyn30A, and Xyn43A with Abf51A.Particular examples of the combination of the hemicellulase as describedherein and other enzyme(s) can include a combination including Xyn5A andAbf51A. In other words, the hemicellulase preparation as describedherein may contain at least Xyn5A.

The other enzyme can be produced in a similar manner with thehemicellulase as described herein. When two or more kinds of enzymes,such as the hemicellulase as described herein and other enzyme(s), areused in combination, these enzymes may be collectively produced, or maybe each independently produced. For example, by co-expressing thehemicellulase as described herein and the enzyme enhancing hemicellulaseactivity in a single host, these enzymes can be collectively produced.

<4> Use of Hemicellulase

The hemicellulase as described herein can be used for the degradation ofhemicellulose. For example, by treating a hemicellulosic substrate withthe hemicellulase as described herein, a saccharification product can beproduced.

The type and number of hemicellulase to be used are not particularlylimited. The number of kinds of hemicellulase to be used may be one ormore, two or more, or three or more. The hemicellulase as describedherein may be used independently, or may be used in combination withcomponent(s) other than the hemicellulase, such as other enzymes. Thehemicellulase as described herein may be used, for example, as a form ofan enzyme preparation containing the hemicellulase, in particular, anenzyme preparation containing the hemicellulase and other enzyme(s).Examples of such an enzyme preparation can include the hemicellulasepreparation as described herein. Examples of the other enzymes caninclude those exemplified above. To the combination of enzymes, thedescriptions concerning the combination of enzymes in the hemicellulasepreparation as described herein can be similarly applied. Thehemicellulase as described herein may be used as a free form, or may beused as an immobilized enzyme immobilized to a solid phase such asresin. When a plurality of enzymes is used, these enzymes maysimultaneously act on a hemicellulosic substrate, or may successively orindependently act on a hemicellulosic substrate.

Examples of the hemicellulosic substrate can include, for example,biomass resources containing hemicellulose. The term “biomass resource”can include cellulosic and/or lignocellulosic biomass produced by plantsor algae and containing a hemicellulose component. Examples of suchbiomass can include, for example, DDGS such as corn DDGS, bagasse, wood,bran, wheat straw, rice straw, rice husk, soybean meal, soybean curdrefuse, coffee grounds, rice bran, etc.

As methods for degrading or hydrolyzing biomass resources, known methodscan be used. For example, the biomass resource may be a dried product ora wet product, and the biomass resource can be preliminarily ground to asize of 100-1000 μm in order to improve treatment efficiency. Thegrounding can be carried out by using a machine such as ball mill,vibration mill, cutter mill, and hammer mill. The ground biomassresource can be suspended in an aqueous medium. Then, to degrade orhydrolyze the biomass resource, the hemicellulase as described hereinand, as required, cellulase can be added to the aqueous medium, and themixture can be heated with stirring. In this method, it is sufficientthat the pH and temperature of the reaction mixture each are within arange in which chosen enzyme(s), such as the hemicellulase as describedherein, is/are not inactivated. For example, usually, when the reactionis carried out under ordinary pressure, the temperature may be within arange of 5 to 70° C., 25 to 60° C., or 35 to 50° C., and the pH may bewithin a range of 3.0 to 10.0, or 5.0 to 8.0. For example, when usingCellic Ctec of Novozymes as cellulase, exemplary conditions can be 35 to55° C. and pH4.5 to 6.0. Examples of the amount of enzyme can include0.1 to 0.5% (w/w TS, total solid). The reaction period can be chosenaccording to the amount of enzyme etc.

The use amount of the hemicellulase as described herein is notparticularly limited, and it may be appropriately chosen by carrying outa preliminarily experiment etc.

By degrading the biomass resource as described above, saccharide(s)is/are generated, that is, a saccharide solution is obtained. Examplesof saccharides can include, for example, glucose, xylose, mannose, andarabinose. Specifically, for example, by saccharifying a hemicellulosecomponent, a saccharide solution containing xylose and arabinose isobtained. Specifically, for example, by saccharifying a cellulosecomponent, a saccharide solution containing glucose is obtained.

The obtained saccharide solution can be used as it is, or after beingsubjected to such a treatment as concentration, dilution, drying,fractionation, purification, and conversion as required, depending onthe use purpose thereof. For example, the obtained saccharide solutioncan be used after isomerization or degradation by chemical reaction orenzymatic reaction. For example, the obtained saccharide solution canalso be used as a dried product after removal of moisture. In addition,component(s) in the saccharide solution can be fractionated and used asrequired. The term “fractionated product” also includes aroughly-purified product and a purified product. Examples of thepurified product can include saccharides such as glucose, xylose,mannose, and arabinose.

The saccharide solution obtained by the aforementioned method, includingprocessed products such as fractionated product, can be used as, forexample, a carbon source for production of an objective substance byfermentation. Examples of the objective substance can include, forexample, alcohols such as methanol, ethanol, propanol, isopropanol,butanol, and butanediol. Other examples of the objective substance caninclude acetic acid, lactic acid, propionic acid, 3-hydroxypropionicacid, succinic acid, citric acid, amino acids, and nucleic acids.

The hemicellulase as described herein can also be used as a component ofan animal feed composition. The term “animal feed composition” may besynonymous to the term “animal feed”. The animal feed composition can beproduced by a usual method using the same components as those of a usualfeed composition depending on the type of the animal to be administeredwith the composition, except that the animal feed composition containsthe hemicellulase as described herein. The animal feed composition asdescribed herein can be obtained by adding the hemicellulase asdescribed herein or the enzyme preparation containing the same, or ananimal feed additive containing the hemicellulase as described hereindescribed below at any stage of production process of a feedcomposition, or by adding and mixing the hemicellulase as describedherein or the enzyme preparation containing the same, or an animal feedadditive containing the hemicellulase as described herein describedbelow with a usual feed composition. One kind of hemicellulase may beused, or two or more kinds of hemicellulases may be used. Feedcomponent(s) other than the hemicellulase is/are not particularlylimited, and can include a biomass resource containing a hemicellulosicsubstrate, such as soybean meal, corn, DDGS, milo, barley, wheat, wheatbran, cassava, and rice bran. The animal feed composition may containother enzyme(s) in addition to the hemicellulase as described herein.Examples of the other enzymes can include amylase, protease, pectinase,phytase, lipase, and the like, as well as the enzymes exemplified above.The animal to be fed with the feed is not particularly limited, andexamples thereof can include ruminants such as cattle, goat, sheep, anddeer; domestic animals such as pig and boar; poultry such as chicken,quail, turkey, duck, and goose; and the like. The form of the feed isnot particularly limited, and the feed may be in any form such as mash,pellet, granule, crumble, flake, and powder.

The hemicellulase as described herein or the enzyme preparationcontaining the same can also be used as an animal feed additive. Theanimal feed additive is typically added and mixed with an animal feedbefore administration of the feed. The animal feed additive may also beadministered to an animal independently of the feed, or the animal feedadditive and the feed as separate ingredients may also be simultaneouslyadministered to an animal. In cases where the animal feed additive isnot mixed with an animal feed before administration as with the lattercase, the animal feed additive can be regarded as an enzyme preparationfor promoting use of the animal feed. The term “animal feed additive”can include such an enzyme preparation.

The animal feed additive may include only the hemicellulase as describedherein or the enzyme preparation containing the same, or may containanother feed additive ingredient. When the other feed additiveingredient is contained, the feed additive (feed additive composition)can be produced by a usual method using the same components as those ofa usual feed additive depending on the type of the animal to beadministered with the additive. The animal feed additive as describedherein can be obtained by adding the hemicellulase as described hereinor the enzyme preparation containing the same at any stage of productionprocess of a feed additive, or by adding and mixing the hemicellulase asdescribed herein or the enzyme preparation containing the same with ausual feed composition. One kind of hemicellulase may be used, or two ormore kinds of hemicellulases may be used in combination.

Examples of the ingredient other than the hemicellulase as describedherein can include carriers, excipients, disintegrants, diluents,antioxidants, binders, nutritional supplement ingredients, agents forpromoting use of nutrients, and the like. Examples of carriers caninclude starch, maltodextrin, calcium carbonate, cyclodextrin, wheat orwheat component, sucrose, glucose, sodium sulfate, talc, polyvinylalcohol, sorbitol, glycerol, benzoate, sorbate, propylene glycol,1,3-propanediol, paraben, sodium chloride, citrate, acetate, phosphate,calcium, pyrosulfite, formate, and the like. Examples of excipients caninclude cellulose such as microcrystalline cellulose, lactose, sodiumcitrate, calcium carbonate, calcium hydrogen phosphate, glycine, starch,lactose, high molecular weight polyethylene glycol, and the like.Examples of disintegrants can include starch, sodium starch glycolate,croscarmellose sodium, certain complex silicate, and the like. Examplesof diluents can include water, ethanol, propylene glycol, glycerin, andthe like. Examples of antioxidants can include ethoxyquin,dibutylhydroxytoluene, butylhydroxyanisole, and the like. Examples ofbinders can include sodium alginate, sodium caseinate, sodiumcarboxymethylcellulose, propylene glycol, sodium polyacrylate, and thelike. Examples of nutritional supplement ingredients can include aminoacids, vitamins, minerals, and the like. Examples of agents forpromoting use of nutrients can include antimicrobial agents,antibiotics, perfumes, taste-imparting agents, enzymes, probiotics, andthe like.

One kind of such an ingredient as mentioned above may be used, or anycombination of plural kinds of such ingredients as mentioned above maybe used. The animal feed additive may contain other enzyme(s) inaddition to the hemicellulase as described herein. Such other enzyme(s)may be the same as those described for the animal feed.

The form of the animal feed additive is not particularly limited, andthe feed additive may be in any form such as mash, pellet, granule,crumble, flake, and powder. When the feed additive has a powdery form,the feed additive can be produced by processing a solution containingthe enzyme as it is or a mixture of such an enzyme solution with suchingredient(s) as mentioned above into a powdery form by spray drying orthe like.

The hemicellulase as described herein, the enzyme preparation containingthe same, and the animal feed additive each may be used as apretreatment agent for a feed before administering the feed to ananimal. Conditions for the pretreatment can be set according to theaforementioned reaction conditions for degradation or saccharificationof a biomass resource.

The amount of the hemicellulase as described herein that is present inthe feed composition (feed) or the feed additive is not particularlylimited, and it can be set according to the type and the amount of thebiomass resource contained in the feed.

EXAMPLES

Hereinafter, the present invention will be more specifically explainedwith reference to the following non-limiting examples.

Example 1: Isolation of Corn NSP-Degrading Microorganisms andIdentification of Strain

(1) Screening of Corn NSP-Degrading Microorganisms by Enrichment Culture

A culture medium containing NSP, an insoluble fiber extract derived fromcorn seed coat (Nisshoku CELLFER, Nihon Shokuhin Kako; “CELLFER” is atrademark of this company), as the sole carbon source was prepared, andenrichment culture was carried out using about 50 kinds of soil samplessampled in Japan. The culture medium for enrichment culture was preparedby dissolving NH₄NO₃ 1.0 g, K₂HPO₄ 1.0 g, NaH₂PO₄.2H₂O 1.3 g, MgSO₄.7H₂O 0.2 g, FeSO₄.7H₂O 0.01 g, MnSO₄.7H₂O 0.01 g, ZnSO₄.7H₂O 0.01 g,CaCl₂).2H₂O 0.01 g, and Nisshoku CELLFER 2 g in ultra pure water to avolume of 1.0 L. The pH of this culture medium was 6.7. Hereinafter,this culture medium is referred to as corn NSP-containing enrichmentculture medium. A solid culture medium obtained by adding agar to thisculture medium is referred to as corn NSP-containing enrichment culturesolid medium. In addition, for the purpose of observing the activity ofxylanase produced by microorganisms grown on the solid medium based onhalo, a culture medium containing 0.5% insoluble xylan derived from Oatspelt (Sigma) instead of Nisshoku CELLFER was prepared. Uponpreparation, xylan particles were homogenized by ultrasonication usingan ultrasonic cleaner (FU-10C, TGK). Hereinafter, this culture medium isreferred to as Oat spelt xylan-containing enrichment culture solidmedium.

One spatulaful of each soil sample was suspended in 1 mL of sterilizedwater, and left to stand for about 1 minute. A 50 μL-aliquot of thesupernatant was collected, and inoculated to 2 mL of the cornNSP-containing enrichment culture medium in a culture test tube. Shakingculture was carried out at 160 rpm at a room temperature using a waterbath shaker PERSONAL-11 (TAITEC). After culturing for 2 weeks or longer,culture test tubes were subjected to visual observations, and test tubesof which the turbidity of the culture medium due to corn NSP was loweredwere selected.

(2) Measurement of Corn NSP Hydrolysis Activity by Dinitrosalicylic AcidMethod

The culture broth was centrifuged (4° C., 20,400×g, 10 minutes), toobtain a culture supernatant. A hydrolysis reaction of corn NSP wascarried out using this culture supernatant, and the amount of generatedreduced termini was quantified by a coloring method usingdinitrosalicylic acid (Sumner, J. B. et al., J. Biol. Chem. 65, 393-395,1925). The procedure is shown below.

Corn NSP (Nisshoku CELLFER) was suspended in 50 mM Britton-Robinsonbuffer adjusted to pH 6.0 to a final concentration of 1.5%. Thissuspension was subjected to ultrasonication for 30 minutes using anultrasonic cleaner, to obtain a substrate solution. An 80 μL-aliquot ofthe substrate solution was added with 20 μL of an enzyme sample (culturesupernatant), and a reaction was carried out at 37° C. for 24 hours.After the enzymatic reaction, the reaction was terminated by addition of100 μL of 1 M NaOH. An insoluble substrate was precipitated bycentrifugation (4° C., 7,000×g, 5 minutes), and 100 μL of a supernatantwas collected. This supernatant (100 μL) was added with 100 μL of acoloring reagent prepared by the method described in Sumner, J. B. etal., and the mixture was boiled at 100° C. for 5 minutes. After coolingwith ice, the mixture was diluted with 550 μL of ultra pure water. Theabsorbance at a wavelength of 545 nm was measured, to quantify theamount of reduced termini generated by hydrolyzation of the substrate.

The corn NSP hydrolysis activity of each culture supernatant wasmeasured as described above, test tubes showing the corn NSP hydrolysisactivity were identified.

(3) Acquisition of Single Clone and Identification of Strain

The culture broths of the test tubes for which the corn NSP hydrolysisactivity were observed were each applied to the corn NSP-containingenrichment culture solid medium, and cultured at a room temperature. Thegrown microorganism was suspended in sterilized water, and seriallydiluted. Each diluted suspension was applied to Oat speltxylan-containing enrichment culture solid medium, and cultured at a roomtemperature. A single clone was obtained on the basis of a halo on thesolid medium due to xylanase activity as an indicator, and designated asH2C strain.

Identification of the H2C strain was carried out on the basis ofmorphological observation, physiological and biochemical property test,and nucleotide sequence analysis of 16S rDNA. It was revealed that thisstrain is a gram-negative bacillus having motility, forms spores, and ispositive for both catalase reaction and oxidase reaction. In addition tothese properties, due to the fact or the like that this strain showed ahigh homology of 94.4 to 97.4% with the nucleotide sequence of the genusPaenibacillus in nucleotide sequence analysis of 16S rDNA, it wasrevealed that this strain should be classified as the genusPaenibacillus. Furthermore, a physiological and biochemical test using abacteria identification test kit API 50 CHB (bioMerieux) was carriedout. As a result, the H2C strain oxidized L-arabinose, D-xylose,glucose, and the like, did not oxidize glycerol, erythritol,D-arabinose, and the like, showed beta-galactosidase activity, did notproduce acetoin, did not hydrolyze gelatin, and did not reduce nitrate.No known species of the genus Paenibacillus perfectly matched with theseproperties was found. From the above, while the H2C strain wasconsidered to be included in the genus Paenibacillus, the results of thenucleotide sequence analysis of 16S rDNA and the physiological andbiochemical property test indicate that the H2C strain is different fromany known species of the genus Paenibacillus, and hence, there may be apossibility that the H2C strain constitutes a novel species of the genusPaenibacillus. Therefore, this strain was designated as Paenibacillussp. H2C strain.

Example 2: Determination of Genome Sequence

The genome sequence of the H2C strain was determined using a nextgeneration sequencer according to the following procedure.

The H2C strain was inoculated to 50 mL of LB medium, and cultured withshaking at 30° C. and 120 rpm for 2 days. Obtained cells were harvestedby centrifugation, and the genomic DNA was extracted using Genomic tip100/G (Qiagen) according to the attached manual. A library was preparedfrom the obtained genomic DNA using Nextera DNA Sample Prep Kit(Illumina), and the genome sequence was analyzed using a next generationsequencer MiSeq v2 (Illumina) and MiSeq Reagent Kit v2 500 cycle(Illumina). ORF prediction and annotation were carried out using GenarisAnnotation System (Genaris). As a result of assembling of the obtainedsequence, 109 contigs were obtained, and a nucleotide sequence of 6,988, 404 bp was determined. As a result of gene identification, 6,128CDSs were predicted.

Example 3: Identification of Enzymes (Xyn5A, Xyn10B, Xyn11A, and Xyn30A)Based on Corn NSP Hydrolysis Activity

The culture supernatant of the H2C strain was fractionated on the basisof the corn NSP hydrolysis activity as an indicator, and enzymes havingthis activity and genes thereof were identified.

(1) Measurement Method of Corn NSP Hydrolysis Activity byPhloroglucinol-Acetate Method

A reaction was carried out using corn NSP (Nisshoku CELLFER) as asubstrate, and the amount of soluble arabinoxylan released from corn NSPwas measured by phloroglucinol-acetate method (Sakka M. et al., Appl.Environ. Microbiol., 77(12):4260-4263, 2011), to thereby evaluate theenzyme activity. The procedure is shown below.

First, Nisshoku CELLFER was suspended in 50 mM Britton-Robinson buffer(pH 6.0) to a final concentration of 2.5%, to obtain a substratesolution. A 400 μL-aliquot of the substrate solution was added with 100μL of an enzyme sample, and a reaction was carried out at 37° C. and pH6.0 for 2 hours. After the enzymatic reaction, the reaction wasterminated by boiling at 100° C. for 5 minutes. An insoluble substratewas precipitated by centrifugation (4° C., 7,000×g, 5 minutes), and 100μL of a supernatant was recovered. Separately, a phloroglucinol-acetatereagent was prepared by mixing 11 mL of acetic acid, 0.2 mL ofhydrochloric acid, 0.5 mL of ethanol solution containing 20%phloroglucinol (Tokyo Kasei), and 0.1 mL of 1.75% glucose solution. Theaforementioned supernatant (100 μL) was added with 500 μL of thephloroglucinol-acetate reagent, and the mixture was boiled at 100° C.for 25 minutes. After cooling with ice, the absorbance at wavelengths of552 nm and 510 nm was measured, and the difference thereof (A₅₅₂-A₅₁₀)was calculated. Similarly, a colorimetric reaction and absorbancemeasurement were carried out using a xylose solution as a standardinstead of the supernatant, and a calibration curve was prepared on thebasis of the A₅₅₂-A₅₁₀ value. The amount of pentose contained in eachsample was calculated using this calibration curve, and taken as theamount of soluble arabinoxylan produced by hydrolysis by the enzymaticreaction.

(2) Preparation of Culture Supernatant of H2C Strain

LB medium was used for culturing the H2C strain. As an inducer, corn NSP(Nisshoku CELLFER) was added to a final concentration of 0.2%. Culturewas carried out with shaking at 30° C. using a shaking culture apparatus(Able, ML-316). After 48 hours, 1.5 L of a culture broth of the H2Cstrain was obtained. The culture broth was centrifuged (4° C., 29,100×g,10 minutes), and the obtained supernatant was subjected to filterfiltration (0.20 μm). Ammonium sulfate was added and dissolved to thesupernatant to a final concentration of 0.7 M, and the resultingprecipitate was removed by centrifugation (4° C., 29,100×g, 10 minutes).The obtained supernatant was subjected to filter filtration (0.20 μm),and used as a starting material for enzyme purification.

(3) Fractionation by Column Chromatography

Fractionation and purification of the enzyme was carried out by acombination of various kinds of column chromatography shown below. Thecorn NSP hydrolysis activity of obtained fractions was measured by thephloroglucinol-acetate method.

(a) Hydrophobic Interaction Chromatography Using HiLoad 16/10Phenylsepharose

The sample was applied to HiLoad 16/10 Phenylsepharose column (GEHealthcare) equilibrated with 0.05 M Tris-HCl buffer (pH 7.0) containing0.7 M ammonium sulfate. After washing the column with the same buffer,adsorbed proteins were eluted with an ammonium sulfate linearconcentration gradient of 0.7 to 0 M.

(b) Anion Exchange Chromatography Using HiTrap Q HP

The buffer of the sample was exchanged for 20 mM Tris-HCl buffer (pH8.0) using a centrifugal filter unit (Amicon Ultra-15, 10 kDa, MerckMillipore). This sample was applied to HiTrap Q HP, 5 mL column (GEHealthcare) equilibrated with the same buffer. After washing the columnwith the same buffer, adsorbed proteins were eluted with an NaCl linearconcentration gradient of 0 to 1 M.

(c) Cation Exchange Chromatography Using HiTrap SP HP

The buffer of the sample was exchanged for 50 mM MES sodium buffer (pH6.0) using Amicon Ultra-15, 10 kDa. This sample was applied to HiTrap SPHP, 5 mL column (GE Healthcare) equilibrated with the same buffer. Afterwashing the column with the same buffer, adsorbed proteins were elutedwith an NaCl linear concentration gradient of 0 to 1 M.

(d) Gel Filtration Chromatography Using HiLoad 16/600 Superdex 200 pg

The sample was concentrated using Amicon Ultra-15, 10 kDa. This samplewas applied to HiLoad 16/600 Superdex 200 pg column (GE Healthcare)equilibrated with 20 mM Tris-HCl buffer (pH 7.0) containing 100 mM NaCl,and eluted with the same buffer.

(4)N-Terminal Amino Acid Sequence Analysis

The sample was concentrated using Amicon Ultra-15, 10 kDa, and separatedby electrophoresis using 4-20% miniprotean TGX precast gel (Bio-Rad).Separated proteins were transferred from the gel to a PVDF membrane (MiniBlot Gel Transfer Stacks, Thermo Fisher Scientific) using iBlot DryBlotting system (Thermo Fisher Scientific), and then stained using CBBStain One (Nacalai Tesque). Bands were excised, and the N-terminal aminoacid sequence was determined using a protein sequencer (Procise 492H,Applied Biosystems).

(5) Purification of Each Enzyme

(a) Xyn5A and Xyn10B

The sample prepared in (2) was subjected to HiLoad 16/10 Phenylsepharosecolumn chromatography. As a result, two fractions eluted at ammoniumsulfate concentrations of 0.05 M and 0.45 M showed a high corn NSPhydrolysis activity. Furthermore, the fraction eluted at an ammoniumsulfate concentration of 0.05 M was collected, subjected to bufferexchange, and then subjected to HiTrap Q HP column chromatography. As aresult, corn NSP hydrolysis activity was confirmed in a non-adsorbedfraction. Furthermore, when this non-adsorbed fraction was subjected toHiTrap SP HP column chromatography, corn NSP hydrolysis activity wasconfirmed in a non-adsorbed fraction. Furthermore, when thisnon-adsorbed fraction was separated by SDS-PAGE, a plurality of bandswas confirmed. As a result of N-terminal amino acid analysis of eachband, partial sequences shown in SEQ ID NO: 1 and SEQ ID NO: 2 wereobtained.

As a result of searching for these partial sequences in proteinsequences presumed to be encoded by the genome of the H2C strain, thepartial sequence shown in SEQ ID NO: 1 matched with the amino acidsequence of positions 1 to 8 of SEQ ID NO: 4 encoded by the nucleotidesequence of SEQ ID NO: 3. Because this protein of SEQ ID NO: 4 has highhomology with proteins of GH family 5, it was designated as Xyn5A. Fromthe result of N-terminal amino acid analysis, it was presumed that theamino acid sequence of the mature protein of Xyn5A corresponds topositions 1 to 535 of SEQ ID NO: 4 and is encoded by the nucleotidesequence of positions 115 to 1719 of SEQ ID NO: 3. In addition, thepartial sequence shown in SEQ ID NO: 2 matched with the amino acidsequence of positions 1 to 15 of SEQ ID NO: 6 encoded by the nucleotidesequence of SEQ ID NO: 5. Because this protein of SEQ ID NO: 6 has highhomology with proteins of GH family 10, it was designated as Xyn10B.From the result of N-terminal amino acid analysis, it was presumed thatthe amino acid sequence of the mature protein of Xyn10B corresponds topositions 1 to 448 of SEQ ID NO: 6 and is encoded by the nucleotidesequence of positions 136 to 1479 of SEQ ID NO: 5. The positions −38 to−1 of SEQ ID NO: 4 and the positions −45 to −1 of SEQ ID NO: 6 arepresumed to be signal peptides.

(b) Xyn11A

A fraction eluted with an ammonium sulfate concentration of 0.45 M inHiLoad 16/10 Phenylsepharose column chromatography in (a) was collected,subjected to buffer exchange, and then subjected to HiTrap SP HP columnchromatography. As a result of subjecting an eluted fraction showingcorn NSP hydrolysis activity to SDS-PAGE, a single band was confirmed.As a result of N-terminal amino acid analysis of this band, a partialsequence shown in SEQ ID NO: 7 was obtained. As a result of searchingfor this partial sequence in protein sequences presumed to be encoded bythe genome of the H2C strain, the partial sequence matched with theamino acid sequence of positions 29 to 38 of SEQ ID NO: 9 encoded by thenucleotide sequence of SEQ ID NO: 8. Because this protein has highhomology with proteins of GH family 11, it was designated as Xyn11A.From the result of N-terminal amino acid analysis, it was presumed thatthe amino acid sequence of the mature protein of Xyn11A corresponds topositions 1 to 183 of SEQ ID NO: 9 and is encoded by the nucleotidesequence of positions 85 to 633 of SEQ ID NO: 8. The positions −28 to −1of SEQ ID NO: 9 are presumed to be a signal peptide.

(c) Xyn30A

As a result of HiTrap SP HP column chromatography in (b), corn NSPhydrolysis activity was confirmed also in a non-adsorbed fraction. Theobtained non-adsorbed fraction was subjected to HiTrap Q HP columnchromatography, and a non-adsorbed fraction was further subjected toHiLoad 16/600 Superdex 200 pg column chromatography. As a result ofsubjecting an eluted fraction showing corn NSP hydrolysis activity toSDS-PAGE, a single band was confirmed. As a result of N-terminal aminoacid analysis of this band, a partial sequence shown in SEQ ID NO: 10was obtained. As a result of searching for this partial sequence inprotein sequences presumed to be encoded by the genome of the H2Cstrain, the partial sequence matched with the amino acid sequence ofpositions 37 to 50 of SEQ ID NO: 12 encoded by the nucleotide sequenceof SEQ ID NO: 11. Because this protein has high homology with proteinsof GH family 30, it was designated as Xyn30A. From the result ofN-terminal amino acid analysis, it was presumed that the amino acidsequence of the mature protein of Xyn30A corresponds to positions 1 to527 of SEQ ID NO: 12 and is encoded by the nucleotide sequence ofpositions 109 to 1689 of SEQ ID NO: 11. The positions −36 to −1 of SEQID NO: 12 are presumed to be a signal peptide.

(d) Xyn43A

As a result of analyzing the genomic sequence of the H2C strain, a geneof an enzyme having high homology with GH family 43 enzymes, and thisenzyme was designated as Xyn43A. As shown in Example 9, it is presumedthat the amino acid sequence of SEQ ID NO: 14 is the amino acid sequenceof Xyn43A precursor (pro sequence). It was presumed that the amino acidsequence of the mature protein of Xyn43A corresponds to positions 1 to608 of SEQ ID NO: 14 and is encoded by the nucleotide sequence ofpositions 79 to 1902 of SEQ ID NO: 13. The positions −26 to −1 of SEQ IDNO: 14 are presumed to be a signal peptide.

Example 4: Preparation of NSP Degrading Enzymes in E. coli

Recombinant enzymes of the four enzymes identified from the culturesupernatant of the H2C strain and the Xyn43A identified by genomeanalysis were prepared. These enzymes are also referred to as NSPdegrading enzymes.

(1) Construction of Expression Strains for Xyn10B, Xyn11A, Xyn30A, andXyn43A

By using the genomic DNA of the H2C strain as a template and primers P1and P2 (SEQ ID NOs: 15 and 16), a region containing a nucleotidesequence encoding Xyn10B was PCR-amplified. PCR-amplification wascarried out using PrimeStar Max (Takara Bio). The reaction solution wasprepared according to the composition attached to the kit, and 30 cyclesof reaction at 98° C. for 10 seconds, 55° C. for 10 seconds, and 68° C.for 10 seconds were carried out. The obtained PCR fragment was ligatedwith pET-21b(+) vector (Merck Millipore) digested with NdeI and XhoIusing In-Fusion HD Cloning Kit (Clontech). E. coli JM109 was transformedwith this ligation reaction solution, and an objective plasmid wasextracted from an ampicillin resistant strain. E. coli BL21(DE3) wastransformed with this plasmid, to obtain an expression strain of Xyn10B.Similarly, an expression strain of Xyn11A was obtained by using primersP3 and P4 (SEQ ID NOs: 17 and 18), an expression strain of Xyn30A wasobtained by using primers P5 and P6 (SEQ ID NOs: 19 and 20), and anexpression strain of Xyn43A was obtained by using primers P7 and P8 (SEQID NOs: 21 and 22). In these expression strains, proteins with His-tagadded to the C-terminus of the mature proteins are expressed for Xyn10B,Xyn11A, and Xyn30A, and a protein with His-tag added to the C-terminusof the precursor protein containing the signal peptide is expressed forXyn43A. Incidentally, it is presumed that the signal peptide of Xyn43Ais cleaved after expression and a mature protein is generated.

(2) Construction of Expression Strain of Xyn5A

By using the genomic DNA of the H2C strain as a template and primers P9and P10 (SEQ ID NOs: 23 and 24), PCR-amplification was carried out underthe same conditions as (1). The obtained PCR fragment was ligated withpETDuet-1 vector (Merck Millipore) digested with BamHI and HindIII usingIn-Fusion HD Cloning Kit (Clontech). E. coli JM109 was transformed withthis ligation reaction solution, and an objective plasmid was extractedfrom an ampicillin resistant strain. E. coli BL21(DE3) was transformedwith this plasmid, to obtain an expression strain of Xyn5A. In thisexpression strain, Xyn5A added with His-tag at the N-terminus isexpressed.

(3) Construction of Expression Strain of Fusarium verticillioidesXylanase in E. coli

As a control, a strain expressing Fvexyn4, a xylanase derived fromFusarium verticillioides described in WO2014/020142, in E. coli wasconstructed, and a purified enzyme was prepared. First, the nucleotidesequence of Fvexyn4 gene described in SEQ ID NO: 6 of WO2014/020142 wascodon-optimized for E. coli, NdeI site was added upstream thereof andXhoI site was added downstream thereof. Synthesis of the resultingnucleotide sequence was outsourced to GenScript, to obtain the resultingnucleotide sequence in a form inserted in EcoRV site of pUC57 vector.Next, the plasmid was treated with the restriction enzymes NdeI andXhoI, subjected to agarose gel electrophoresis, and a DNA fragmentcontaining the Fvexyn4 gene was recovered from the gel. The DNA fragmentwas ligated to pET21-b(+) treated with NdeI and XhoI using DNA LigationKit (Takara Bio), to prepare an expression plasmid. E. coli JM109 wastransformed with this ligation reaction solution, and an objectiveplasmid was extracted from an ampicillin resistant strain. E. coliBL21(DE3) was transformed with this plasmid, to obtain an expressionstrain of Fvexyn4. In this expression strain, Fvexyn4 added with His-tagat the C-terminus is expressed.

(4) Purification of Recombinant Enzymes

Each expression strain was grown in LB medium containing 100 mg/Lampicillin at 37° C. for 6 hours. A 1.6 mL-aliquot of the obtainedculture broth was inoculated into 160 mL of Overnight Express Instant TBMedium (Merck) containing 100 mg/L ampicillin, and shaking culture wascarried out using a Sakaguchi flask. The culture conditions were set to30° C. for 18 hours for Xyn5A and Xyn30A, and 18° C. for 40 hours forXyn11A, Xyn10B, Xyn43A, and FveXyn4.

After completion of the culture, cells were harvested from the obtainedculture broth by centrifugation, suspended in a buffer solutionconsisting of 20 mM Tris-HCl (pH 7.6), 300 mM NaCl, and 10 mM imidazole,and subjected to ultrasonic disruption. Cell debris was removed from thedisrupted solution by centrifugation, and the obtained supernatant wastaken as a soluble fraction.

The obtained soluble fraction was applied to a His-tag proteinpurification column HisTALON Superflow Cartridge (CV=5 mL, Clontech;HisTALON and Superflow are trademarks of this company) equilibrated withthe aforementioned buffer solution, to allow adsorption on the carrier.Proteins not adsorbed on the carrier (non-adsorbed proteins) were washedoff with the aforementioned buffer solution, and then adsorbed proteinswere eluted with a solution identical to the aforementioned buffersolution except that imidazole concentration was changed to 150 mM at aflow rate of 5 mL/min.

Eluted fractions containing the enzyme were collected, andbuffer-exchanged into 50 mM Britton-Robinson buffer (pH 6.0) usingAmicon Ultra-15, 10 kDa, to obtain a purified enzyme solution.

As a control, xylanase was purified from Econase XT (ABVista; Econase isa trademark of this company), which is commercially available as a feedenzyme, according to the method of WO2014/020142.

The concentration of each obtained purified enzyme was measured usingProtein Assay Lowry Kit (Nacalai Tesque) with Quick Start BSA Standardset (Bio-Rad) as a standard.

Example 5: Evaluation of Beta-1,4-Xylanase Activity of Xyn5A, Xyn10B,Xyn11A, and Xyn30A

Xylanase activity of each purified enzyme of Xyn5A, Xyn10B, Xyn11A, andXyn30A prepared in Example 4 was evaluated. Beechwood-derived solublexylan (Sigma, X4252) and insoluble wheat arabinoxylan (Megazyme,P-WAXYI) were used as a substrate for activity evaluation, and theamount of reducing termini generated by the enzymatic reaction wasevaluated. Each of these substrates is a polysaccharide havingbeta-1,4-linked xylose as the main chain. The procedure is shown below.

First, these substrates were each suspended in 50 mM Britton-Robinsonbuffer adjusted to pH 6.0 to a final concentration of 1.875%, and thesuspension was subjected to ultrasonication for 30 minutes using anultrasonic cleaner, to obtain a substrate solution. An 80 μL-aliquot ofthis substrate solution was added with 20 μL of a diluted solution ofthe purified enzyme solution prepared in Example 4, and a reaction wascarried out at 37° C. for 10 minutes. As a blank sample, the reactionwas carried out using 50 mM Britton-Robinson buffer (pH 6.0) instead ofthe enzyme solution. After the enzymatic reaction, the reaction wasterminated by addition of 100 μL of 1 M NaOH. An insoluble substrate wasprecipitated by centrifugation (4° C., 20,400×g, 10 minutes), and asupernatant was recovered. The amount of reduced termini in thissupernatant was quantified by the dinitrosalicylic acid method in thesame manner as in Example 1. A colorimetric reaction and absorbancemeasurement were similarly carried out using a xylose solution as astandard, to prepare a calibration curve. The amount of reduced terminigenerated by hydrolysis of the substrate was quantified using thiscalibration curve. The amount of reduced termini in the blank sample wassubtracted from the amount of reduced termini in each sample, tocalculate the amount of reduced termini generated by the enzymaticreaction.

The reducing termini-generating activity of each NSP-degrading enzyme isshown in Table 1. Xyn5A showed the reducing termini-generating activityonly against insoluble wheat arabinoxylan, and Xyn30A showed thereducing termini-generating activity only against beechwood xylan.Xyn10B and Xyn11A showed the reducing termini-generating activityagainst both substrates. These results revealed that these four enzymeshave beta-1,4-xylanase activity.

TABLE 1 Reducing termini-generating activity against each substrate(μmol/min/mg) Insoluble Beechwood wheat xylan arabinoxylan Xyn5A   0.00 4.62 Xyn10B 85.9  41.1  Xyn11A 140.5  43.7  Xyn30A 17.6   0.00

Example 6: Evaluation of Alpha-L-Arabinofuranosidase Activity of Xyn43A

It has been reported that GH family 43, to which Xyn43A is considered tobelong, has alpha-L-arabinofuranosidase activity which releases sidechain arabinose from arabinoxylan (Lagaert et al., BiotechnologyAdvances 32, 316-332, 2014). Therefore, in order to confirm thearabinofuranosidase activity possessed by Xyn43A, insoluble wheatarabinoxylan (Megazyme, P-WAXYI) decomposition reaction by Xyn43A wascarried out, to evaluate the release of arabinoxylan. Wheat arabinoxylanhas a structure in which arabinofuranose (arabinose) residues are boundto the xylan main chain via α-1,2 bond and/or α-1,3 bond.

An enzymatic reaction using insoluble wheat arabinoxylan as a substratewas carried out using a diluted solution of the purified enzyme solutionof Xyn43A prepared in Example 4 in the same manner as in Example 5, anda supernatant was recovered. This supernatant was diluted, and separatedusing an ion chromatograph for saccharide analysis (Thermo FisherScientific, Dionex ICS-5000+). CarboPac SA10-4 μm (Thermo FisherScientific) was used as the column, and 1 mM potassium hydroxide wasused for elution. Separated saccharides were detected by pulsedamperometric detection (PAD) method. Separately, standards for xylose,arabinose, and glucose were separated under the same conditions, and theconcentration of each component contained in the sample was quantified.

The results are shown in FIG. 1. A peak was detected at the sameretention time as that of the arabinose standard in the reactionsupernatant after the reaction using Xyn43A, whereas no peak wasdetected in the blank sample. From the above, it was shown that Xyn43Ahas alpha-L-arabinofuranosidase activity. The amount of generatedarabinose was quantified, and the arabinose release activity per enzymeweight was calculated to be 2.0 μmol/min/mg.

Example 7: Evaluation of Corn NSP Degradation Activity of Each NSPDegrading Enzyme

(1) DDGS Decomposition Reaction

Regarding the activity of each NSP degrading enzyme, the activity todecompose and solubilize insoluble arabinoxylan contained in corn wasevaluated. The procedure is shown below.

First, corn DDGS, which is commercially available as a feed, waspulverized, and then passed through a sieve of 0.25 mm mesh. Next, inorder to preliminarily remove soluble arabinoxylan contained in the cornDDGS, 500 mg of the corn DDGS was weighed in a 50 mL tube (Falcon),suspended in 20 mL of distilled water, and stirred at 37° C. for 30minutes. DDGS was recovered by centrifugation (8,000 rpm, 10 minutes),and the supernatant was removed.

The recovered DDGS was suspended in 10 mL of 100 mM Britton-Robinsonbuffer (pH 6.5), and added with distilled water to a volume of 18 mL.This DDGS suspension was dispensed into 1.5 mL tubes by 0.45 mL per tubewhile stirring. The purified enzyme solution prepared in Example 4 wasdiluted with 50 mM Britton-Robinson buffer (pH 6.5) to a finalconcentration of 100 μg-protein/mL, to obtain a diluted enzyme solution.The diluted enzyme solution was dispensed into the DDGS suspension inthe 1.5 mL tubes by 0.05 mL per tube so that the total amount became 0.5mL (the enzyme concentration in the reaction solution was 10 μg/mL, theDDGS concentration in the reaction solution was about 25 mg/mL). Thesetubes were placed on a rotator and agitated for 5 hours in an incubatorat 37° C., to carry out decomposition reaction of DDGS. A reaction wascarried out in triplicate for each enzyme. As a control, a reaction inwhich 50 mM Britton-Robinson buffer (pH 6.5) was added instead of thediluted enzyme solution was also carried out. In addition, in order toevaluate the effect of mixing enzymes, a reaction was also carried outusing a composition in which two kinds of diluted enzyme solutions weremixed in equal amounts (each enzyme was contained 5 μg/mL in thereaction solution, and the total enzyme concentration was 10 μg/mL).

After the reaction, the reaction was terminated by heating each tube at100° C. for 2 minutes. Furthermore, the reaction solution wascentrifugally filtered using Ultrafree-MC Centrifugal Filter Unit (MerckMillipore) having a pore diameter of 0.22 μm to remove DDGS, and afiltrate was recovered and used as a soluble fraction.

(2) Measurement of Amount of Arabinoxylan Contained in Soluble Fraction

The soluble fraction was mixed with 0.4 M sulfuric acid, and hydrolyzedby heating at 125° C. for 1 hr. This hydrolysate was separated using anion chromatograph for saccharide analysis in the same manner as inExample 6, and the concentrations of xylose and arabinose werequantified. The total value of the concentrations of xylose andarabinose contained in the soluble fraction was taken as the freearabinoxylan concentration.

The results are shown in FIG. 2 (N=3, error bars each represent standarddeviation). It was confirmed that all of the NSP degrading enzymesderived from Paenibacillus sp. H2C strain had the activity of releasingarabinoxylan from corn DDGS. In addition, it was shown that all of theseenzymes are able to release a larger amount of arabinoxylan as comparedto the xylanase purified from Econase XT. Furthermore, mixing ofdifferent enzymes enabled release of a larger amount of arabinoxylanthan that observed when one enzyme was allowed to act solely.

Example 8: Evaluation of Addition Concentration of NSP Degrading Enzymeand Free Arabinoxylan Concentration

In order to evaluate the relationship between the enzyme concentrationand the free arabinoxylan concentration from DDGS, the corn DDGSdegradation activity under conditions of enzyme concentration lower thatin Example 7 was evaluated.

The reaction was carried out in the same manner as in Example 7(1),using a solution obtained by diluting the purified enzyme solutionprepared in Example 4 to a final concentration of 0.1 μg/mL or 1 μg/mL(the enzyme concentration in the reaction solution is 10 ng/mL or 100ng/mL). In addition, the arabinoxylan concentration contained in thesoluble fraction was quantified by the same method as in Example 7(2).

The results are shown in FIG. 3 (N=3, error bars each represent standarddeviation). It was shown that Xyn5A release a larger amount ofarabinoxylan from DDGS as compared to FveXyn4 under any conditions ofenzyme concentrations of 10 ng/mL or 100 ng/mL.

Example 9: Analysis of N-Terminus of Xyn43A Mature Protein

Xyn43A purified in the same manner as in Example 4 was concentrated byultrafiltration, subjected to SDS-PAGE using Mini-Protean TGX PrecastGels 4-20% (Bio-Rad), and then transferred to a PVDF membrane usingiBlot Gel Transfer Stacks (Thermo Fisher Scientific) and iBlot DryBlotting system. The PVDF membrane was stained using CBB (CBB Stain One,Nacalai Tesque), a band was excised, and the N-terminal amino acidsequence of 10 amino acids was determined using a protein sequencer(Procise 492H, Applied Biosystems). The result is shown in SEQ ID NO:25. As a result of comparison with the amino acid sequence of Xyn43Ashown in SEQ ID NO: 14, 7 amino acids matched with the amino acidsequence of positions 27 to 36 from the N terminus (positions 1 to 10 inSEQ ID NO: 14). From the above, it was inferred that cleavage occursbetween Ala at position 26 from the N terminus (position −1 in SEQ IDNO: 14) and Ala at position 27 from the N terminus (position 1 in SEQ IDNO: 14), to thereby generate a mature protein. A possible example of thereason why the amino acid sequences do not completely match iscontamination of the purified enzyme with the precursor.

Example 10: Preparation of Xyn5A Homologues in E. coli

(1) Acquisition of Amino Acid Sequences of P1XP2_GH5, JDR-2_GH5, andBcGH5

In order to search for enzymes having the same function as Xyn5A of theH2C strain, a search based on BlastP(blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins) was carried out fordatabases of published sequence information using the amino acidsequence of Xyn5A mature protein as a query, to thereby obtain aminoacid sequences highly homologous to the amino acid sequence of Xyn5A. Asfor these amino acid sequences, the secretory signal peptide sequencewas predicted using SignalP (cbs.dtu.dk/services/SignalP). Three of themare shown in Table 2. The enzymes of these amino acid sequences weredesignated as P1XP2_GH5, JDR-2_GH5, and BcGH5. In the table, the columntitled “Identity” shows the amino acid sequence identity to Xyn5A.

TABLE 2 Sequences highly homologous to Xyn5A Amino acid sequence (signalNucleotide sequence/ sequence Enzyme Accession Identity mature (maturename Source number (%) protein) protein) P1XP2_ Paenibacillus KHF37231.183 SEQ ID SEQ ID GH5 sp. P1XP2 NO: 26 NO: 27 (positions (positions −29to −1/ 88 to 1695) positions 1 to 536) JDR-2_ Paenibacillus ACT02895.182 SEQ ID SEQ ID GH5 sp. JDR-2 NO: 28 NO: 29 (positions (positions −32to −1/ 97 to 1704) positions 1 to 536) BcGH5 Bacillus SDZ01154.1 77 SEQID SEQ ID caseinilyticus NO: 30 NO: 31 (positions (positions −29 to −1/88 to 1695) positions 1 to 536)

(2) Construction of Expression Strains of P1XP2_GH5, JDR-2_GH5, andBcGH5 in E. coli

The nucleotide sequence encoding the precursor proteins of P1XP2_GH5,JDR-2_GH5, and BcGH5 were codon-optimized for E. coli, NdeI site wasadded upstream thereof and XhoI site was added downstream thereof.Synthesis of the resulting nucleotide sequences was outsourced toEurofins Genomics, to obtain the resulting nucleotide sequences in aform inserted in pTAKN-2 vector for P1XP2_GH5 and JDR-2_GH5, or inpEX-K4J1 vector for BcGH5. Next, the plasmids were each treated with therestriction enzymes NdeI and XhoI, subjected to agarose gelelectrophoresis, and a DNA fragment containing each gene was recoveredfrom the gel. The DNA fragment was ligated to pET21-b(+) treated withNdeI and XhoI using DNA Ligation Kit (Takara Bio), to prepare anexpression plasmid. E. coli JM109 was transformed with this ligationreaction solution, and an objective plasmid was extracted from anampicillin resistant strain. E. coli BL21(DE3) was transformed withthese plasmids, to obtain expression strains of P1XP2_GH5, JDR-2_GH5,and BcGH5. In these expression strains, the precursor proteins ofP1XP2_GH5, JDR-2_GH5, and BcGH5 including a signal peptide and addedwith His-tag at the C-terminus are expressed. Incidentally, it ispresumed that these signal peptides are cleaved after expression andmature proteins are generated.

(3) Purification of Recombinant Enzymes

Each expression strain was grown in LB medium containing 100 mg/Lampicillin at 37° C. for 6 hours. A 1.6 mL-aliquot of the obtainedculture broth was inoculated into 160 mL of Overnight Express Instant TBMedium (Merck) containing 100 mg/L ampicillin, and shaking culture wascarried out using a Sakaguchi flask. The culture conditions were set to30° C. for 18 hours.

After completion of the culture, cells were harvested from the obtainedculture broth by centrifugation, suspended in a buffer solutionconsisting of 20 mM Tris-HCl (pH 7.6), 300 mM NaCl, and 10 mM imidazole,and subjected to ultrasonic disruption. Cell debris was removed from thedisrupted solution by centrifugation, and the obtained supernatant wastaken as a soluble fraction.

The obtained soluble fraction was applied to a His-tag proteinpurification column HisTALON Superflow Cartridge (CV=5 mL, Clontech;HisTALON and Superflow are trademarks of this company) equilibrated withthe aforementioned buffer solution, to allow adsorption on the carrier.Proteins not adsorbed on the carrier (non-adsorbed proteins) were washedoff with the aforementioned buffer solution, and then adsorbed proteinswere eluted with a solution identical to the aforementioned buffersolution except that imidazole concentration was changed to 150 mM at aflow rate of 5 mL/min.

Eluted fractions containing the enzyme were collected, andbuffer-exchanged into 50 mM Britton-Robinson buffer (pH 6.0) usingAmicon Ultra-15, 10 kDa, to obtain a purified enzyme solution.

The concentration of each purified enzyme obtained was measured usingProtein Assay Lowry Kit (Nacalai Tesque) with Quick Start BSA Standardset (Bio-Rad) as a standard.

Example 11: Evaluation of Beta-1,4-Xylanase Activity of P1XP2_GH5,JDR-2_GH5, and BcGH5

Xylanase activity of each purified enzyme of P1XP2_GH5, JDR-2_GH5, andBcGH5 prepared in Example 10 was evaluated. Insoluble wheat arabinoxylan(Megazyme, P-WAXYI) was used as a substrate for activity evaluation, andthe amount of reducing termini generated by the enzymatic reaction wasevaluated. The procedure is shown below.

First, these substrates were each suspended in 50 mM Britton-Robinsonbuffer adjusted to pH 6.0 to a final concentration of 1.875%, and thesuspension was subjected to ultrasonication for 30 minutes using anultrasonic cleaner, to obtain a substrate solution. An 80 μL-aliquot ofthis substrate solution was added with 20 μL of a diluted solution ofthe purified enzyme solution prepared in Example 10, and a reaction wascarried out at 37° C. for 10 minutes. As a blank sample, the reactionwas carried out using 50 mM Britton-Robinson buffer (pH 6.0) instead ofthe enzyme solution. After the enzymatic reaction, the reaction wasterminated by addition of 100 μL of 1 M NaOH. An insoluble substrate wasprecipitated by centrifugation (4° C., 20,400×g, 10 minutes), and asupernatant was recovered. The amount of reduced termini in thissupernatant was quantified by the dinitrosalicylic acid method in thesame manner as in Example 1. A colorimetric reaction and absorbancemeasurement were similarly carried out using a xylose solution as astandard, to prepare a calibration curve. The amount of reduced terminigenerated by hydrolysis of the substrate was quantified using thiscalibration curve. The amount of reduced termini in the blank sample wassubtracted from the amount of reduced termini in each sample, tocalculate the amount of reduced termini generated by the enzymaticreaction.

The reducing termini-generating activity of each enzyme is shown inTable 3. All of these enzymes showed the reducing termini-generatingactivity, and hence, it was revealed that these three enzymes havebeta-1,4-xylanase activity.

TABLE 3 Reducing termini-generating activity of each enzyme againstwheat arabinoxylan Activity (μmol/ Enzyme name min/mg) P1XP2_GH5 20.0JDR-2_GH5 21.5 BcGH5 20.8

Example 12: Evaluation of Corn NSP Degradation Activity of P1XP2_GH5,JDR-2_GH5, and BcGH5

The reaction was carried out in the same manner as in Example 7(1),using each of solutions obtained by diluting the purified enzymesolution of Xyn5A prepared in Example 4 and the purified enzymesolutions prepared in Example 10 to a final concentration of 10 μg/mL(the enzyme concentration in the reaction solution is 1 μg/mL). However,the reaction period was changed to 2 hours. In addition, thearabinoxylan concentration contained in the soluble fraction wasquantified by the same method as in Example 7(2).

The results are shown in FIG. 4 (N=2, error bars each represent standarddeviation). All of these enzymes released a larger amount ofarabinoxylan than that observed for the case of the reaction withoutaddition of enzyme (blank), and hence, it was revealed that they have anactivity of releasing arabinoxylan from DDGS.

Example 13: Preparation of Xyn30A Homologues in E. coli

(1) Acquisition of Amino Acid Sequences of TCA20 GH30 and BaGH30

In order to search for enzymes having the same function as Xyn30A of theH2C strain, a search based on BlastP(https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins) was carried outfor databases of published sequence information using the amino acidsequence of Xyn30A mature protein as a query, to thereby obtain aminoacid sequences highly homologous to the amino acid sequence of Xyn30A.As for these amino acid sequences, the secretory signal peptide sequencewas predicted using GENETYX Ver. 10 (Genetyx). Two of them are shown inTable 4. The enzymes of these amino acid sequences were designated asTCA20_GH30 and BaGH30. In the table, the column titled “Identity” showsthe amino acid sequence identity to Xyn30A.

TABLE 4 Sequences highly homologous to Xyn30A Amino acid sequence(signal Nucleotide sequence/ sequence Enzyme Accession Identity mature(mature name Source number (%) protein) protein) TCA20_ PaenibacillusGAK42763.1 75 SEQ ID SEQ ID GH30 sp. TCA20 NO: 32 NO: 33 (positions(positions −30 to −1/ 91 to 1677) positions 1 to 529) BaGH30 BacillusKJD54725.1 78 SEQ ID SEQ ID amylo- NO: 34 NO: 35 liquefaciens (positions(positions −30 to −1/ 91 to 1260) positions 1 to 390)

(2) Construction of Expression Strains of TCA20_GH30 and BaGH30 in E.coli

The nucleotide sequence encoding the mature proteins of TCA20 GH30 andBaGH30 were codon-optimized for E. coli, NdeI site was added upstreamthereof and XhoI site was added downstream thereof. Synthesis of theresulting nucleotide sequences was outsourced to Eurofins Genomics, toobtain the resulting nucleotide sequences in a form inserted in pEX-K4J1vector. Next, the plasmids were each treated with the restrictionenzymes NdeI and XhoI, subjected to agarose gel electrophoresis, and aDNA fragment containing each gene was recovered from the gel. The DNAfragment was ligated to pET21-b(+) treated with NdeI and XhoI using DNALigation Kit (Takara Bio), to prepare an expression plasmid. E. coliJM109 was transformed with this ligation reaction solution, and anobjective plasmid was extracted from an ampicillin resistant strain. E.coli BL21(DE3) was transformed with these plasmids, to obtain expressionstrains of TCA20 GH30 and BaGH30. In these expression strains, themature proteins of TCA20 GH30 and BaGH30 added with His-tag at theC-terminus are expressed.

(3) Purification of Recombinant Enzymes

Purified enzyme solutions were prepared using the expression strainsconstructed in (2) in the same manner as that in Example 10(3).

Example 14: Evaluation of Beta-1,4-Xylanase Activity of TCA20 GH30 andBaGH30

Xylanase activity of each purified enzyme of TCA20 GH30 and BaGH30prepared in Example 13 was evaluated. Beechwood-derived xylan (Sigma,X4252) was used as a substrate for activity evaluation, and theevaluation was carried out in the same manner as that in Example 11.

The reducing termini-generating activity of each enzyme is shown inTable 5. All of these enzymes showed the reducing termini-generatingactivity, and hence, it was revealed that these two enzymes havebeta-1,4-xylanase activity.

TABLE 5 Reducing termini-generating activity of each enzyme againstbeechwood-derived xylan Activity (μmol/ Enzyme name min/mg) TCA20_GH3027.3 BaGH30 24.0

Example 15: Evaluation of corn NSP degradation activity of TCA20 GH30and BaGH30

The reaction was carried out in the same manner as in Example 7(1),using each of solutions obtained by diluting the purified enzymesolution of Xyn30A prepared in Example 4 and the purified enzymesolutions prepared in Example 13 to a final concentration of 10 μg/mL(the enzyme concentration in the reaction solution is 1 μg/mL). However,the reaction period was changed to 2 hours. In addition, thearabinoxylan concentration contained in the soluble fraction wasquantified by the same method as in Example 7(2).

The results are shown in FIG. 5 (N=2, error bars each represent standarddeviation). All of these enzymes released a larger amount ofarabinoxylan than that observed for the case of the reaction withoutaddition of enzyme (blank), and hence, it was revealed that they have anactivity of releasing arabinoxylan from DDGS.

Example 16: Preparation of Abf51A in E. coli

(1) Acquisition of Sequence of Abf51A

As a result of analyzing the genomic sequence of the H2C strain, a geneof an enzyme having high homology with GH family 51 enzymes, and thisenzyme was designated as Abf51A. The amino acid sequence of Abf51Aprecursor (pro sequence) is presumed to be SEQ ID NO: 36. As for thisamino acid sequence, the secretory signal peptide sequence was predictedusing GENETYX Ver. 10 (Genetyx). It was presumed that the amino acidsequence of the mature protein of Abf51A corresponds to positions 1 to469 of SEQ ID NO: 36 and is encoded by the nucleotide sequence ofpositions 82 to 1488 of SEQ ID NO: 37. The positions −27 to −1 of SEQ IDNO: 36 are presumed to be a signal peptide.

Construction of Expression Strain for Abf51A

By using the genomic DNA of the H2C strain as a template and primers P11and P12 (SEQ ID NOs: 38 and 39), a region containing a nucleotidesequence encoding Abf51A was PCR-amplified. PCR-amplification wascarried out using PrimeStar Max (Takara Bio). The reaction solution wasprepared according to the composition attached to the kit, and 30 cyclesof reaction at 98° C. for 10 seconds, 55° C. for 10 seconds, and 68° C.for 10 seconds were carried out. The obtained PCR fragment was ligatedwith pET-21b(+) vector (Merck Millipore) digested with NdeI and XhoIusing In-Fusion HD Cloning Kit (Clontech). E. coli JM109 was transformedwith this ligation reaction solution, and an objective plasmid wasextracted from an ampicillin resistant strain. E. coli BL21(DE3) wastransformed with this plasmid, to obtain an expression strain of Abf51A.In this expression strain, a protein with His-tag added to theC-terminus of the mature protein is expressed. Incidentally, it ispresumed that the signal peptide of Abf51A is cleaved after expressionand a mature protein is generated.

Purification of Recombinant Enzyme

The expression strain of Abf51A was cultured overnight at 37° C. usingLB medium, and the culture broth was inoculated into fresh LB medium inan amount of 1% (v/v). Once the strain was cultured at 37° C. to reachan exponential growth phase (0D660 was about 0.40 to 0.60),isopropyl-β-D-thiogalactopyranoside (IPTG, Nacalai Tesque) at a finalconcentration of 0.5 mM was added. The culture was further continued at18° C. for 18 hours, to induce expression of the objective gene. Cellsharvested by centrifugation (4° C., 6,900×g, 10 minutes) were suspendedin 50 mM Britton-Robinson buffer (pH 6.5). The cells were disruptedusing an ultrasonicator Bioruptor UCD-250 (Cosmo Bio), then centrifugedagain (4° C., 20,400×g, 10 minutes), and the obtained supernatant wastaken as a cell-free extract.

The cell-free extract was purified by a batch method using Ni Sepharose6 Fast Flow (GE Healthcare), which is a nickel-immobilized carrier forpurifying His-tag proteins. The binding buffer used was 50 mM Tris-HClbuffer (pH 7.5) containing 25 mM imidazole, and the elution buffer usedwas 50 mM Tris-HCl buffer (pH 7.5) containing 500 mM imidazole. First,133 μL of 75%-slurried carrier was taken in a 1.5 mL microtube, washedwith sterilized ion exchange water and the binding buffer in volumes of2.5 times the volume of the carrier, and then equilibrated with an equalvolume of the binding buffer. Next, the sample was added to the carrier,and gently stirred at 4° C. for 30 minutes using a rotator (Aikuru,Iwaki). The carrier was washed three times with 5 volume of the bindingbuffer, and then eluted three times with 2 volume of the elution buffer.The elution fraction dialyzed against 10 mM Britton-Robinson buffer (pH6.5) was taken as a purified enzyme solution.

The concentration of the obtained purified enzyme was quantified. TheLowry method (DC Protein Assay, Bio-Rad) was used for proteinquantification. The protein concentration was calculated on the basis ofa calibration curve prepared using bovine serum albumin (BSA, Sigma) asa standard substance.

Example 17: Evaluation of Wheat Arabinoxylan Degradation Activity ofAbf51A and Xyn5A

Insoluble arabinoxylan derived from wheat (WAX, Megazyme, P-WAXYI) wassuspended in 50 mM Britton-Robinson buffer (pH 6.5) to a finalconcentration of 1.2%, to obtain a substrate solution. A 80 μL-aliquotof this substrate solution was mixed with 10 μL of 2.15 pmol/mL Abf51Apurified enzyme solution, 10 μL of 2.68 pmol/μL Xyn5A purified enzymesolution (Example 4), or both, filled up to 100 μL, and a reaction wascarried out at pH 6.5 and 37° C. After the enzymatic reaction, thereaction was terminated by addition of 100 μL of 1 M NaOH. An insolublesubstrate was precipitated by centrifugation (4° C., 20,400×g, 10minutes), and a supernatant was recovered. The amount of reduced terminigenerated by hydrolysis of the substrate in this supernatant wasquantified by the dinitrosalicylic acid method.

The results are shown in FIG. 6 (N=2). Addition of both of Abf51A andXyn5A provided a higher absorbance than that observed when each enzymewas added solely, and hence, showed a synergistic effect on degradationof wheat arabinoxylan.

Example 18: Evaluation of Corn NSP Degradation Activity of Abf51A andXyn5A

Corn NSP (Nisshoku CELLFER) was suspended in 50 mM Britton-Robinsonbuffer (pH 6.5) to a final concentration of 3.125%, to obtain asubstrate solution. A 400 μL-aliquot of this substrate solution wasmixed with 50 μL of 2.15 pmol/mL Abf51A purified enzyme solution, 50 μLof 2.68 pmol/μL Xyn5A purified enzyme solution (Example 4), or both,filled up to 500 μL, and a reaction was carried out at pH 6.5 and 37° C.After the enzymatic reaction, the reaction was terminated by boiling for2 minutes. An insoluble substrate was precipitated by centrifugation (4°C., 20,400×g, 20 minutes), and a supernatant was recovered. The amountof arabinoxylan in this supernatant was quantified by thephloroglucinol-acetate method.

The results are shown in FIG. 7 (N=2). Addition of both of Abf51A andXyn5A provided a larger value of the difference between absorbance at552 nm and absorbance at 510 nm than that observed when each enzyme wasadded solely, and hence, showed a synergistic effect on degradation ofcorn NSP.

INDUSTRIAL APPLICABILITY

According to the present invention, hemicellulase that degrades corn NSPis provided. This hemicellulase is useful for, for example, saccharideproduction from biomass resources.

<Explanation of Sequence Listing>

SEQ ID NOS:

1: Partial amino acid sequence of Xyn5A protein of Paenibacillus sp. H2C

2: Partial amino acid sequence of Xyn10B protein of Paenibacillus sp.H2C

3: Nucleotide sequence of Xyn5A gene of Paenibacillus sp. H2C

4: Amino acid sequence of Xyn5A protein of Paenibacillus sp. H2C

5: Nucleotide sequence of Xyn10B gene of Paenibacillus sp. H2C

6: Amino acid sequence of Xyn10B protein of Paenibacillus sp. H2C

7: Partial amino acid sequence of Xyn11A protein of Paenibacillus sp.H2C

8: Nucleotide sequence of Xyn11A gene of Paenibacillus sp. H2C

9: Amino acid sequence of Xyn11A protein of Paenibacillus sp. H2C

10: Partial amino acid sequence of Xyn30A protein of Paenibacillus sp.H2C

11: Nucleotide sequence of Xyn30A gene of Paenibacillus sp. H2C

12: Amino acid sequence of Xyn30A protein of Paenibacillus sp. H2C

13: Nucleotide sequence of Xyn43A gene of Paenibacillus sp. H2C

14: Amino acid sequence of Xyn43A protein of Paenibacillus sp. H2C

15 to 24: Primers

25: Partial amino acid sequence of Xyn43A protein of Paenibacillus sp.H2C

26: Amino acid sequence of P1XP2_GH5 protein of Paenibacillus sp. P1XP2

27: Nucleotide sequence of P1XP2_GH5 gene of Paenibacillus sp. P1XP2

28: Amino acid sequence of JDR-2_GH5 protein of Paenibacillus sp. JDR-2

29: Nucleotide sequence of JDR-2_GH5 gene of Paenibacillus sp. JDR-2

30: Amino acid sequence of BcGH5 protein of Bacillus caseinilyticus

31: Nucleotide sequence of BcGH5 gene of Bacillus caseinilyticus

32: Amino acid sequence of TCA20 GH30 protein of Paenibacillus sp. TCA20

33: Nucleotide sequence of TCA20 GH30 gene of Paenibacillus sp. TCA20

34: Amino acid sequence of BaGH30 protein of Bacillus amyloliquefaciens

35: Nucleotide sequence of BaGH30 gene of Bacillus amyloliquefaciens

36: Amino acid sequence of Abf51A protein of Paenibacillus sp. H2C

37: Nucleotide sequence of Abf51A gene of Paenibacillus sp. H2C

38 to 39: Primers

1. A composition comprising a first protein and a second protein, saidfirst and second proteins are each selected from the group consisting ofprotein (A), protein (B), protein (C), and protein (D); wherein protein(A) is selected from the group consisting of: (A1) a protein comprisingthe amino acid sequence of positions 1 to 535 of SEQ ID NO: 4, positions1 to 536 of SEQ ID NO: 26, positions 1 to 536 of SEQ ID NO: 28, orpositions 1 to 536 of SEQ ID NO: 30, wherein said protein hashemicellulase activity; (A2) a protein comprising the amino acidsequence of positions 1 to 535 of SEQ ID NO: 4, positions 1 to 536 ofSEQ ID NO: 26, positions 1 to 536 of SEQ ID NO: 28, or positions 1 to536 of SEQ ID NO: 30, but which includes substitution, deletion,insertion, and/or addition of 1 to 10 amino acid residues, wherein saidprotein has hemicellulase activity; and (A3) a protein comprising anamino acid sequence showing an identity of 90% or higher to the aminoacid sequence of positions 1 to 535 of SEQ ID NO: 4, positions 1 to 536of SEQ ID NO: 26, positions 1 to 536 of SEQ ID NO: 28, or positions 1 to536 of SEQ ID NO: 30, wherein said protein has hemicellulase activity;wherein protein (B) is selected from the group consisting of: (B1) aprotein comprising the amino acid sequence of positions 1 to 527 of SEQID NO: 12, positions 1 to 529 of SEQ ID NO: 32, or positions 1 to 390 ofSEQ ID NO: 34, wherein said protein has hemicellulase activity, (B2) aprotein comprising the amino acid sequence of positions 1 to 527 of SEQID NO: 12, positions 1 to 529 of SEQ ID NO: 32, or positions 1 to 390 ofSEQ ID NO: 34, but which includes substitution, deletion, insertion,and/or addition of 1 to 10 amino acid residues, wherein said protein hashemicellulase activity, and (B3) a protein comprising an amino acidsequence showing an identity of 90% or higher to the amino acid sequenceof positions 1 to 527 of SEQ ID NO: 12, positions 1 to 529 of SEQ ID NO:32, or positions 1 to 390 of SEQ ID NO: 34, wherein said protein hashemicellulase activity; wherein the protein (C) is a hemicellulase ofglucoside hydrolase family 10; and where in the protein (D) is ahemicellulose of glucoside hydrolase family
 11. 2. The compositionaccording to claim 1, wherein said proteins (A), (B), (C), and (D) eachhave beta-1,4-xylanase activity.
 3. The composition according to claim1, wherein the proteins of (A2) and (A3) each comprise the amino acidsequence of positions 218 to 239 of SEQ ID NO:
 4. 4. (canceled)
 5. Ahemicellulase preparation comprising a protein selected from the groupconsisting of proteins (A), (B), (C), (D), and combinations thereof;wherein the protein (A) is selected from the group consisting of: (A1) aprotein comprising the amino acid sequence of positions 1 to 535 of SEQID NO: 4, positions 1 to 536 of SEQ ID NO: 26, positions 1 to 536 of SEQID NO: 28, or positions 1 to 536 of SEQ ID NO: 30, wherein said proteinhas hemicellulase activity, (A2) a protein comprising the amino acidsequence of positions 1 to 535 of SEQ ID NO: 4, positions 1 to 536 ofSEQ ID NO: 26, positions 1 to 536 of SEQ ID NO: 28, or positions 1 to536 of SEQ ID NO: 30, but which includes substitution, deletion,insertion, and/or addition of 1 to 10 amino acid residues, wherein saidprotein has hemicellulase activity, and (A3) a protein comprising anamino acid sequence showing an identity of 90% or higher to the aminoacid sequence of positions 1 to 535 of SEQ ID NO: 4, positions 1 to 536of SEQ ID NO: 26, positions 1 to 536 of SEQ ID NO: 28, or positions 1 to536 of SEQ ID NO: 30, wherein said protein has hemicellulase activity;wherein the protein (B) is selected from the group consisting of: (B1) aprotein comprising the amino acid sequence of positions 1 to 527 of SEQID NO: 12, positions 1 to 529 of SEQ ID NO: 32, or positions 1 to 390 ofSEQ ID NO: 34, wherein said protein has hemicellulase activity, (B2) aprotein comprising the amino acid sequence of positions 1 to 527 of SEQID NO: 12, positions 1 to 529 of SEQ ID NO: 32, or positions 1 to 390 ofSEQ ID NO: 34, but which includes substitution, deletion, insertion,and/or addition of 1 to 10 amino acid residues, wherein said protein hashemicellulase activity, and (B3) a protein comprising an amino acidsequence showing an identity of 90% or higher to the amino acid sequenceof positions 1 to 527 of SEQ ID NO: 12, positions 1 to 529 of SEQ ID NO:32, or positions 1 to 390 of SEQ ID NO: 34, wherein said protein hashemicellulase activity; wherein the protein (C) is a hemicellulase ofglucoside hydrolase family 10; and wherein the protein (D) is ahemicellulase of glucoside hydrolase family
 11. 6. The hemicellulasepreparation according to claim 5, wherein the protein comprises a firstprotein and a second protein each selected from the group consisting ofthe proteins (A), (B), (C), and (D).
 7. The hemicellulase preparationaccording to claim 5, further comprising a protein selected from thegroup consisting of: (F1) a protein comprising the amino acid sequenceof positions 1 to 469 of SEQ ID NO: 36, wherein said protein has aproperty of enhancing hemicellulase activity; (F2) a protein comprisingthe amino acid sequence of positions 1 to 469 of SEQ ID NO: 36, butwhich includes substitution, deletion, insertion, and/or addition of 1to 10 amino acid residues, wherein said protein has a property ofenhancing hemicellulase activity; and (F3) a protein comprising an aminoacid sequence showing an identity of 90% or higher to the amino acidsequence of positions 1 to 469 of SEQ ID NO: 36, wherein said proteinhas a property of enhancing hemicellulase activity.
 8. (canceled)
 9. ADNA encoding the protein according to claim
 1. 10. A vector containingthe DNA according to claim
 9. 11. A host having enhanced expression ofthe DNA according to claim
 9. 12. The host according to claim 11, whichis a bacterium or a fungus.
 13. A method for producing asaccharification product, the method comprising: treating ahemicellulosic substrate with the protein according to claim
 1. 14. Themethod according to claim 13, wherein the hemicellulosic substrate is abiomass resource.
 15. An animal feed additive comprising a proteinselected from the group consisting of proteins (A), (B), (C), (D), andcombinations thereof; wherein the protein (A) is selected from the groupconsisting of: (A1) a protein comprising the amino acid sequence ofpositions 1 to 535 of SEQ ID NO: 4, positions 1 to 536 of SEQ ID NO: 26,positions 1 to 536 of SEQ ID NO: 28, or positions 1 to 536 of SEQ ID NO:30, wherein said protein has hemicellulase activity, (A2) a proteincomprising the amino acid sequence of positions 1 to 535 of SEQ ID NO:4, positions 1 to 536 of SEQ ID NO: 26, positions 1 to 536 of SEQ ID NO:28, or positions 1 to 536 of SEQ ID NO: 30, but which includessubstitution, deletion, insertion, and/or addition of 1 to 10 amino acidresidues, wherein said protein has hemicellulase activity; and (A3) aprotein comprising an amino acid sequence showing an identity of 90% orhigher to the amino acid sequence of positions 1 to 535 of SEQ ID NO: 4,positions 1 to 536 of SEQ ID NO: 26, positions 1 to 536 of SEQ ID NO:28, or positions 1 to 536 of SEQ ID NO: 30, wherein said protein hashemicellulase activity; wherein the protein (B) is selected from thegroup consisting of: (B1) a protein comprising the amino acid sequenceof positions 1 to 527 of SEQ ID NO: 12, positions 1 to 529 of SEQ ID NO:32, or positions 1 to 390 of SEQ ID NO: 34, wherein said protein hashemicellulase activity; (B2) a protein comprising the amino acidsequence of positions 1 to 527 of SEQ ID NO: 12, positions 1 to 529 ofSEQ ID NO: 32, or positions 1 to 390 of SEQ ID NO: 34, but whichincludes substitution, deletion, insertion, and/or addition of 1 to 10amino acid residues, wherein said protein has hemicellulase activity;and (B3) a protein comprising an amino acid sequence showing an identityof 90% or higher to the amino acid sequence of positions 1 to 527 of SEQID NO: 12, positions 1 to 529 of SEQ ID NO: 32, or positions 1 to 390 ofSEQ ID NO: 34, wherein said protein has hemicellulase activity; whereinthe protein (C) is a hemicellulase of glucoside hydrolase family 10; andwherein the protein (D) is a hemicellulase of glucoside hydrolase family11.
 16. The animal feed additive according to claim 15, furthercomprising a protein selected from the group consisting of: (F1) aprotein comprising the amino acid sequence of positions 1 to 469 of SEQID NO: 36, wherein said protein has a property of enhancinghemicellulase activity; (F2) a protein comprising the amino acidsequence of positions 1 to 469 of SEQ ID NO: 36, but which includessubstitution, deletion, insertion, and/or addition of 1 to 10 amino acidresidues, wherein said protein has a property of enhancing hemicellulaseactivity; and (F3) a protein comprising an amino acid sequence showingan identity of 90% or higher to the amino acid sequence of positions 1to 469 of SEQ ID NO: 36, wherein said protein has a property ofenhancing hemicellulase activity.
 17. An animal feed comprising at leastone protein selected from the group consisting of proteins (A), (B),(C), and (D), wherein the protein (A) is selected from the groupconsisting of: (A1) a protein comprising the amino acid sequence ofpositions 1 to 535 of SEQ ID NO: 4, positions 1 to 536 of SEQ ID NO: 26,positions 1 to 536 of SEQ ID NO: 28, or positions 1 to 536 of SEQ ID NO:30, wherein said protein has hemicellulase activity; (A2) a proteincomprising the amino acid sequence of positions 1 to 535 of SEQ ID NO:4, positions 1 to 536 of SEQ ID NO: 26, positions 1 to 536 of SEQ ID NO:28, or positions 1 to 536 of SEQ ID NO: 30, but which includessubstitution, deletion, insertion, and/or addition of 1 to 10 amino acidresidues, wherein said protein has hemicellulase activity; and (A3) aprotein comprising an amino acid sequence showing an identity of 90% orhigher to the amino acid sequence of positions 1 to 535 of SEQ ID NO: 4,positions 1 to 536 of SEQ ID NO: 26, positions 1 to 536 of SEQ ID NO:28, or positions 1 to 536 of SEQ ID NO: 30, wherein said protein hashemicellulase activity; wherein the protein (B) is selected from thegroup consisting of: (B1) a protein comprising the amino acid sequenceof positions 1 to 527 of SEQ ID NO: 12, positions 1 to 529 of SEQ ID NO:32, or positions 1 to 390 of SEQ ID NO: 34, wherein said protein hashemicellulase activity; (B2) a protein comprising the amino acidsequence of positions 1 to 527 of SEQ ID NO: 12, positions 1 to 529 ofSEQ ID NO: 32, or positions 1 to 390 of SEQ ID NO: 34, but whichincludes substitution, deletion, insertion, and/or addition of 1 to 10amino acid residues, wherein said protein has hemicellulase activity;and (B3) a protein comprising an amino acid sequence showing an identityof 90% or higher to the amino acid sequence of positions 1 to 527 of SEQID NO: 12, positions 1 to 529 of SEQ ID NO: 32, or positions 1 to 390 ofSEQ ID NO: 34, wherein said protein has hemicellulase activity; whereinthe protein (C) is a hemicellulase of glucoside hydrolase family 10; andwherein the protein (D) is a hemicellulase of glucoside hydrolase family11.
 18. The animal feed according to claim 17, further comprising aprotein selected from the group consisting of: (F1) a protein comprisingthe amino acid sequence of positions 1 to 469 of SEQ ID NO: 36, whereinsaid protein has a property of enhancing hemicellulase activity; (F2) aprotein comprising the amino acid sequence of positions 1 to 469 of SEQID NO: 36, but which includes substitution, deletion, insertion, and/oraddition of 1 to 10 amino acid residues, wherein said protein has aproperty of enhancing hemicellulase activity; (F3) a protein comprisingan amino acid sequence showing an identity of 90% or higher to the aminoacid sequence of positions 1 to 469 of SEQ ID NO: 36, wherein saidprotein has a property of enhancing hemicellulase activity. 19.(canceled)
 20. The composition according to claim 1, wherein the firstprotein is selected from the group consisting of the proteins (A) and(B), and wherein the second protein is selected from the groupconsisting of the proteins (C) and (D).
 21. The composition according toclaim 1, wherein the first protein is selected from the group consistingof the proteins (A) and (B), and wherein the second protein is theprotein (C).
 22. The composition according to claim 1, wherein theprotein (C) is selected from the group consisting of: (C1) a proteincomprising the amino acid sequence of positions 1 to 448 of SEQ ID NO:6, wherein said protein has hemicellulase activity; (C2) a proteincomprising the amino acid sequence of positions 1 to 448 of SEQ ID NO:6, but which includes substitution, deletion, insertion, and/or additionof 1 to 10 amino acid residues, wherein said protein has hemicellulaseactivity; and (C3) a protein comprising an amino acid sequence showingan identity of 90% or higher to the amino acid sequence of positions 1to 448 of SEQ ID NO: 6, wherein said protein has hemicellulase activity;wherein the protein (D) is selected from the group consisting of: (D1) aprotein comprising the amino acid sequence of positions 1 to 183 of SEQID NO: 9, wherein said protein has hemicellulase activity; (D2) aprotein comprising the amino acid sequence of positions 1 to 183 of SEQID NO: 9, but which includes substitution, deletion, insertion, and/oraddition of 1 to 10 amino acid residues, wherein said protein hashemicellulase activity; and (D3) a protein comprising an amino acidsequence showing an identity of 90% or higher to the amino acid sequenceof positions 1 to 183 of SEQ ID NO: 9, wherein said protein hashemicellulase activity.
 23. The composition according to claim 1,comprising the protein (B), wherein the protein (B) is selected from thegroup consisting of: (B1a) a protein comprising the amino acid sequenceof positions 1 to 527 of SEQ ID NO: 12, wherein said protein hashemicellulase activity; (B2a) a protein comprising the amino acidsequence of positions 1 to 527 of SEQ ID NO: 12, but which includessubstitution, deletion, insertion, and/or addition of 1 to 10 amino acidresidues, wherein said protein has hemicellulase activity; and (B3a) aprotein comprising an amino acid sequence showing an identity of 90% orhigher to the amino acid sequence of positions 1 to 527 of SEQ ID NO:12, wherein said protein has hemicellulase activity.
 24. Thehemicellulase preparation according to claim 6, wherein the firstprotein is selected from the group consisting of the proteins (A) and(B), and wherein the second protein is selected from the groupconsisting of the proteins (C) and (D).
 25. The hemicellulasepreparation according to claim 6, wherein the first protein is selectedfrom the group consisting of the proteins (A) and (B), and wherein thesecond protein is the protein (C).
 26. The hemicellulase preparationaccording to claim 5, wherein the protein (C) is selected from the groupconsisting of: (C1) a protein comprising the amino acid sequence ofpositions 1 to 448 of SEQ ID NO: 6, wherein said protein hashemicellulase activity; (C2) a protein comprising the amino acidsequence of positions 1 to 448 of SEQ ID NO: 6, but which includessubstitution, deletion, insertion, and/or addition of 1 to 10 amino acidresidues, wherein said protein has hemicellulase activity; and (C3) aprotein comprising an amino acid sequence showing an identity of 90% orhigher to the amino acid sequence of positions 1 to 448 of SEQ ID NO: 6,wherein said protein has hemicellulase activity; wherein the protein (D)is selected from the group consisting of: (D1) a protein comprising theamino acid sequence of positions 1 to 183 of SEQ ID NO: 9, wherein saidprotein has hemicellulase activity; (D2) a protein comprising the aminoacid sequence of positions 1 to 183 of SEQ ID NO: 9, but which includessubstitution, deletion, insertion, and/or addition of 1 to 10 amino acidresidues, wherein said protein has hemicellulase activity; and (D3) aprotein comprising an amino acid sequence showing an identity of 90% orhigher to the amino acid sequence of positions 1 to 183 of SEQ ID NO: 9,wherein said protein has hemicellulase activity.
 27. The hemicellulasepreparation according to claim 5, comprising the protein (B), whereinthe protein (B) is selected from the group consisting of: (B1a) aprotein comprising the amino acid sequence of positions 1 to 527 of SEQID NO: 12, wherein said protein has hemicellulase activity; (B2a) aprotein comprising the amino acid sequence of positions 1 to 527 of SEQID NO: 12, but which includes substitution, deletion, insertion, and/oraddition of 1 to 10 amino acid residues, wherein said protein hashemicellulase activity; and (B3a) a protein comprising an amino acidsequence showing an identity of 90% or higher to the amino acid sequenceof positions 1 to 527 of SEQ ID NO: 12, wherein said protein hashemicellulase activity.
 28. The animal feed additive according to claim15, wherein the protein comprises a first protein and a second protein,wherein the first and second proteins are each selected from the groupconsisting of the proteins (A), (B), (C), and (D).
 29. The animal feedadditive according to claim 28, wherein the first protein is selectedfrom the group consisting of the proteins (A) and (B), and wherein thesecond protein is selected from the group consisting of the proteins (C)and (D).
 30. The animal feed additive according to claim 28, wherein thefirst protein is selected from the group consisting of the proteins (A)and (B), and wherein the second protein is the protein (C).
 31. Theanimal feed additive according to claim 15, wherein the protein (C) isselected from the group consisting of: (C1) a protein comprising theamino acid sequence of positions 1 to 448 of SEQ ID NO: 6, wherein saidprotein has hemicellulase activity; (C2) a protein comprising the aminoacid sequence of positions 1 to 448 of SEQ ID NO: 6, but which includessubstitution, deletion, insertion, and/or addition of 1 to 10 amino acidresidues, wherein said protein has hemicellulase activity; and (C3) aprotein comprising an amino acid sequence showing an identity of 90% orhigher to the amino acid sequence of positions 1 to 448 of SEQ ID NO: 6,wherein said protein has hemicellulase activity; wherein the protein (D)is selected from the group consisting of: (D1) a protein comprising theamino acid sequence of positions 1 to 183 of SEQ ID NO: 9, wherein saidprotein has hemicellulase activity; (D2) a protein comprising the aminoacid sequence of positions 1 to 183 of SEQ ID NO: 9, but which includessubstitution, deletion, insertion, and/or addition of 1 to 10 amino acidresidues, wherein said protein has hemicellulase activity; and (D3) aprotein comprising an amino acid sequence showing an identity of 90% orhigher to the amino acid sequence of positions 1 to 183 of SEQ ID NO: 9,wherein said protein has hemicellulase activity.
 32. The animal feedadditive according to claim 15, comprising the protein (B), wherein theprotein (B) is selected from the group consisting of: (B1a) a proteincomprising the amino acid sequence of positions 1 to 527 of SEQ ID NO:12, wherein said protein has hemicellulase activity; (B2a) a proteincomprising the amino acid sequence of positions 1 to 527 of SEQ ID NO:12, but which includes substitution, deletion, insertion, and/oraddition of 1 to 10 amino acid residues, wherein said protein hashemicellulase activity; and (B3a) a protein comprising an amino acidsequence showing an identity of 90% or higher to the amino acid sequenceof positions 1 to 527 of SEQ ID NO: 12, wherein said protein hashemicellulase activity.
 33. The animal feed according to claim 17,wherein the protein comprises a first protein and a second protein,wherein the first and second proteins are each selected from the groupconsisting of the proteins (A), (B), (C), and (D).
 34. The animal feedaccording to claim 33, wherein the first protein is selected from thegroup consisting of the proteins (A) and (B), and wherein the secondprotein is selected from the group consisting of the proteins (C) and(D).
 35. The animal feed according to claim 33, wherein the firstprotein is selected from the group consisting of the proteins (A) and(B), and wherein the second protein is the protein (C).
 36. The animalfeed according to claim 17, wherein the protein (C) is selected from thegroup consisting of: (C1) a protein comprising the amino acid sequenceof positions 1 to 448 of SEQ ID NO: 6, wherein said protein hashemicellulase activity; (C2) a protein comprising the amino acidsequence of positions 1 to 448 of SEQ ID NO: 6, but which includessubstitution, deletion, insertion, and/or addition of 1 to 10 amino acidresidues, wherein said protein has hemicellulase activity; and (C3) aprotein comprising an amino acid sequence showing an identity of 90% orhigher to the amino acid sequence of positions 1 to 448 of SEQ ID NO: 6,wherein said protein has hemicellulase activity; wherein the protein (D)is selected from the group consisting of: (D1) a protein comprising theamino acid sequence of positions 1 to 183 of SEQ ID NO: 9, wherein saidprotein has hemicellulase activity; (D2) a protein comprising the aminoacid sequence of positions 1 to 183 of SEQ ID NO: 9, but which includessubstitution, deletion, insertion, and/or addition of 1 to 10 amino acidresidues, wherein said protein has hemicellulase activity; and (D3) aprotein comprising an amino acid sequence showing an identity of 90% orhigher to the amino acid sequence of positions 1 to 183 of SEQ ID NO: 9,wherein said protein has hemicellulase activity.
 37. The animal feedaccording to claim 17, comprising the protein (B), wherein the protein(B) is selected from the group consisting of: (B1a) a protein comprisingthe amino acid sequence of positions 1 to 527 of SEQ ID NO: 12, whereinsaid protein has hemicellulase activity; (B2a) a protein comprising theamino acid sequence of positions 1 to 527 of SEQ ID NO: 12, but whichincludes substitution, deletion, insertion, and/or addition of 1 to 10amino acid residues, wherein said protein has hemicellulase activity;and (B3a) a protein comprising an amino acid sequence showing anidentity of 90% or higher to the amino acid sequence of positions 1 to527 of SEQ ID NO: 12, wherein said protein has hemicellulase activity.